If you have patience, you could always use Star Fleet Battles
, that's what it was designed for! Plus, you will be a hard core TOS purist.
Though I love SFB, in my opinion Federation Commander would probably be the best to use for RPG combat, as in worse-case scenarios, you could end up a single combat taking up an entire session, or maybe even spilling into 2, with SFB.
Also, FC has less rules for people to get familiar with, so would not recommend SFB unless all your players know it and play it already.