Updated from 12:58 p.m. EDT

Bank of America's

(BAC) - Get Report

decision to part ways with three former

Countrywide Financial

executives after its acquisition of the mortgage lender last year is a silver lining in the dark cloud perpetually hovering over CEO Ken Lewis.

The

Securities and Exchange Commission

has accused the russet-skinned former Countrywide CEO Angelo Mozilo of misleading investors about the risks involved in its mortgage lending operations while selling off stock for a $140 million profit. The agency is charging former COO and president David Sambol and former CFO Eric Sieracki with fraud as well.

Thankfully, this mess didn't happen on BofA's watch -- which BofA is happy to point out.

"It would be inappropriate for us to comment since those named in the enforcement action were not employed by the company following our acquisition in July 2008," BofA spokeswoman Shirley Norton said.

Countrywide has actually performed well under the Charlotte, N.C., bank's umbrella since it was acquired at the start of 2008, as it was about to cave under the pressure of escalating losses from the "toxic" loans Mozilo referenced in

email correspondence

cited in the SEC complaint.

Following the acquisition, Bank of America halted its subprime lending operations, wrote down much of the toxic debt, and eventually halted foreclosures and began modifying better loans as part of the Obama administration's plan to keep families in their homes. All this was not only to benefit the U.S. consumer: The Countrywide purchase helped quadruple BofA's revenue during the first quarter, as refinancing activity surged.

The firm didn't estimate how much Countrywide ultimately contributed to its bottom line. Still, the acquisition "added to net income as mortgage lending and refinancing volume increased," despite continued loan losses and integration costs.

Jason Polun, who analyzes BofA at T. Rowe Price, noted the company's recent success in quickly raising nearly $34 billion that government stress tests determined it needed. "That was a big deal," he says.

"The earnings were pretty good, the stress test came out better than expected, and they're likely to sell off a couple more businesses to raise more capital," Polun adds. "But they've come a long way and the progress is meaningful."

Unfortunately, few are touting BofA's successes in the same fashion. They are focused instead on missteps related to its acquisition of the troubled investment bank Merrill Lynch, whose results, not incidentally, contributed nearly 90% to BofA's first-quarter profit.

So why are shareholders still railing for Lewis' replacement, and why is Congress hauling him in for further questioning?

Some factions of frustrated shareholder allege that Lewis obfuscated key information about Merrill, while charging ahead with the acquisition. However, Lewis' hands were not exactly untied, since then-Treasury Secretary Henry Paulson and

Federal Reserve

Chairman Ben Bernanke reportedly pressured the CEO into sealing the deal.

Lewis ultimately did, accepting another $20 billion in federal loans to cover impending losses on Merrill's books. He has already testified about the deal in front of lawmakers, answered questions from New York Attorney General Andrew Cuomo, and met with scores of shareholders, both privately and at the firm's annual meeting in April. But, according to a report in the

Wall Street Journal

, he will be back in Washington again on Thursday to explain possible discrepancies among all of those many statements and disclosures. He will also have to outline what BofA has been doing with all its billions of dollars in government funds, the

Journal

reports.

The government also required all firms accepting government funds to review top managers for potential replacements, and CtW Investment Group, an investor consortium that represents pension funds, issued another call for Lewis' resignation on Tuesday.

BofA has answered the demand of regulators and shareholders with several key changes to the board and executive ranks. The latest came late Friday afternoon, when

BofA with the announcement of four new board members.

Those moves followed the departure of longtime director O. Temple Sloan and the replacement of Chief Risk Officer Amy Woods Brinkley by another internal executive, Gregory Curl, 60. Director Robert Tillman is also leaving the bank amid a U.S.-mandated review, casting the spotlight once again on the government's role in decision making at the lender.

All of this comes after Lewis was stripped of his chairman title as a result of a shareholder vote on April 29. His replacement, Walter Massey, has been leading a detailed review of top ranks. But his selection is also predictive of more change afoot since Massey is within a year of the mandatory retirement age himself.

The Federal Deposit Insurance Corp. is reported to be closely scrutinizing the management changes at BofA, whose leadership ranks are notoriously insular. Even after shareholders deposed Lewis of his chairman role, the board stood behind the embattled executive, who has pledged to stay with the firm until it begins paying back TARP funds.

Of course, BofA is not alone among the big financial firms that received government assistance, and added scrutiny. While leadership at

JPMorgan Chase

(JPM) - Get Report

,

Wells Fargo

(WFC) - Get Report

,

Goldman Sachs

(GS) - Get Report

and

Morgan Stanley

(MS) - Get Report

have remained intact,

Citigroup

(C) - Get Report

CEO

Vikram Pandit is reportedly under pressure, and

General Motors

(GM) - Get Report

,

Fannie Mae

(FNM)

,

Freddie Mac

(FRE)

and

American International Group

(AIG) - Get Report

chiefs were forced out by the government for hand-picked candidates.

But BofA has a tendency to hang onto the talent it plans to retain. The company may have pushed out Brinkley -- an easy target who was criticized for her handling of risk through the crisis -- to keep Curl within the executive ranks. A similar move was made at the end of last year, when then-general counsel Timothy Mayopoulos was pushed out of the role in favor of Brian Moynihan, who is widely viewed as a potential successor to Lewis.

Jonathan S. Finger, a managing partner of Finger Interests, one of the firms trying to shake up the boardroom, sees recent changes as "positive." He thinks the government-mandated management review is also a necessary step, as long as BofA isn't pressured by micromanaging regulators to make selections that hurt its business.

But critics contest that the government's drastic intervention into financial firms is only blocking Bank of America's path to recovery. Julia Plotts, who teaches finance and economics at the University of Southern California, says shareholders -- not regulators -- should be the ones controlling BofA's directions, policies and activities.

"All of this government influence and scrutiny has killed the company and continues to affect its ability to recover," says Plotts. "I wonder if Ken Lewis had acted in the best interests of his shareholders and walked away from the Merrill deal where the company would be right now. I tend to think we wouldn't be having this discussion."

The changes also call into question how Bank of America's operations will be affected. BofA, the largest U.S. bank by assets, is working through two mammoth integrations amid an ongoing recession. The firm is also seeking funds beyond the required $33.9 billion related to the stress-test gap, in order to repay $45 billion in TARP funds as soon as possible.

Lewis has built his career at Bank of America, spending more than eight years as CEO, with a tight-knit group of advisers and managers surrounding him. While independent voices may encourage positive change, integrating a wave of new leaders with new visions, while integrating all the other massive changes, may create more tension than it resolves.

"If you shoot too many people at dawn and they seem like random shootings of your executives, you might give people concern that there's no one at the helm," says Dale Stanway, a senior consultant at management firm Hay Group, who has worked with several financial firms. "On the flip side of it, I think it's pretty clear it's a whole new world for financial institutions, especially financial institutions that have received government aid."