Geary was probably told "If Michael gets indicted, then you are finished" (i.e. the dead hooker story comes out). It would have been political and personal suicide for Geary to have double-crossed Micheal.

Maybe he didn't know about Pentangelli (if Roth knew that Geary belonged to Michael, maybe he got Questadt, who sits closer to the chairman and is therefore more senior (?-in any case, Geary is suffciently unimportant to be allowed to clear off to chair his own meeting) to persuade the chairman to keep Pentangelli under wraps for security reasons). Or perhaps Frankie had not at that point agreed to the deal?

The "few bad apples" that Geary referred to was Willy Cicci and any other l.c.n. members already convicted? So he meant that Michael should not be tarnished with the same brush (to mix metaphors) not that Michael was one of the bad apples.