I personally think that if/when the Conspiracy bugs return for another round, they will find it much more difficult to infiltrate Starfleet, the Federation government, or Section 31, because after the first time, and the Changling threat during the Dominion War, Starfleet will probably have come up with ways to better sniff them out, and if certain people start acting suspicious, well they may check. I wouldn't be surprise if they invented ways of dealing with the parasites (such as beaming them out of the infected individual, similar to how they beamed Gou'lds from those they latched onto), in case they ever returned.
I see it more likely that they will try to infiltrate less secure populations, such as distant colonies, and get them to do their bidding. War eventually breaks out with the bugs, and the issue is how does Starfleet deal with this issue? Do they treat them like any enemy, and destroy their ships, the bugs, and their hosts along with them? Or do they attempt to disable the bug's ships, try to rescue the victims from their captors, possibly at the risk of giving the bugs a chance to gain an upper hand? At which point should Starfleet be willing to allow collateral damage, and risk destroying the bugs along with those who they infected?