There are a few missions in which you are facing Federation officers who have been taken over by enemy mind control (e.g. Undine control). Also, during the time-travel mission in the Devidian Feature Episode series you will be fighting against Federation officers.
BTW: does anybody here know if kills of Mirror Universe Terran Federation enemies count towards these accolades, or are they accounted for separately?
The mission "War Games" is, as far as I know, the only one to give ground Fed kills.
I might be wrong, but I think it is "Crack in the Mirror" where you can get space Fed kills. There are three ships near the end that count as Fed (don't know why) so you have to kill two of them, warp out, and warp back in again many times before you complete the accolade.