I dunno. M3 was a critical time for the Theseus.
If any of the pilots were Cylons, they could of caused a great deal of damage even beyond what already happened.
The attack would of probably been timed to ensure that the Cylon pilot(s) were on CAP duty or otherwise up in the air when the initial sabotage occurred. One Cylon in a viper would of meant that the Theseus would be down at least two birds - one of these losses being a Viper or Raptor switching sides, the other being the human-controlled Viper that gets shot down by a sneak attack from his 'wingman'. Cue the boarding parties actually getting through due to a lack of vipers providing cover, and the Theseus getting captured instead of destroyed because doing so opens up interesting possibilities for the Cylons...
Memes aside, I doubt any of the pilots are/were Cylons. M3 would of played out too differently if that was the case.