The note, which was distributed shortly after the market closed on Monday, came on the heels of SAC's $1.8 billion settlement with federal prosecutors over charges that it routinely engaged in insider trading over the years. As part of the settlement, which is subject to two judges' approval, SAC agreed to plead guilty to four counts of securities fraud and to give up its registration as a public investment advisor. The firm now has up to five years to return its remaining $4 billion or so in outside capital, a substantial, but minority amount, of its more than $13 billion overall.
(Read more: SAC agrees to end advisory business, pay $1.8 billion in plea pact)
In Monday's staff e-mail, Conheeney said the settlement would not change SAC's ability to trade internal capital. "We anticipate that our registration will be revoked by the SEC," he wrote, referring to the Securities and Exchange Commission, "but it will not affect our ability to operate as a family office."
SAC management has privately expressed a desire to win back its investment-advisor registration at some point in the future, said a person familiar with the matter. But resurfacing as a public-investor vehicle, even after time has passed may be unlikely in light of a pending SEC case against Cohen, who has been charged in civil court with failing to supervise errant employees. In the e-mail Monday, Conheeney described those charges as being "without merit."
In the first portion of the staff e-mail, Conheeney explained that SAC had settled with the Justice Department because under U.S. law, "a company can be charged because of criminal activity by an employee, even one acting without the knowledge of the company's management and in violation of its well-understood procedures, practices, and institutions." Given all of that, SAC acknowledges its "corporate responsibility for the handful of former employees … whose criminal conduct triggered the firm's liability."
Conheeney also thanked SAC's staff of more than 900 employees worldwide for staying on board. "That so many of you have stuck by the firm is extremely gratifying," he wrote. "On behalf of Steve and senior management, thank you."
—By CNBC's Kate Kelly. Follow her on Twitter