Since Thompson's arrival, Yahoo co-founder from Yahoo's board and was quickly by board chairman Roy Bostock and three other directors.

Brad Shimmin, an analyst with CurrentAnalysis, said the incident may more be embarrassing than devastating to Yahoo.

"I don't think this will ultimately damage Yahoo's ability to regain its relevancy within the marketplace," Shimmin said. "As we've seen with all such crises of corporate faith, so long as the board acts quickly and with authority in resolving issues like this, Yahoo will be able to regain any ground lost."

Thompson, however, may be facing a longer road.

"Unfortunately, his future is not in his hands," said Shimmin. "If he takes ownership and responsibility for the discrepancies, there is no reason he cannot regain trust that has been lost. However, assuming the allegations are true, regardless of his actions, the board may still choose to resolve the issue by making Mr. Thompson go away."