Good question, LW. Several answers possible:
I think whatever "brother" relationship twixt Tom and Michael had all but disappeared after that penultimate boathouse humiliation, which occurred before Fredo's murder. In fact, you could make a case that part of the motivation for Fredo's murder was Michael firing a shot across Tom's bows--"You got an offer [maybe even solicited an offer, as Olivant said]? Nobody leaves me--brother or no. Look at Fredo."

I also believe that Tom's abiding characteristic, loyalty, took over whatever misgivings he may have had about Fredo's murder. And, not to put too fine a point on it, Tom's options were limited, by his lack of experience outside the family business, and by the fact that Michael would never let him go. Tom, even better than Michael, knew that, as long as he was "house counsel" to the Corleones, law enforcement would have to tread carefully in moving against him and Michael due to attorney/client privilege and the fact that bar associations are vigorous in protecting their own kind. Cut loose from the Corleones, Tom would be fair game for law enforcement pressure against him and his former client.