My suggestion is to use the "Warp Button" as a forfeit mission option while in a mission. Sort of like leaving the map in SFC 2/OP. That way we can have plasma, missiles, etc and bring the fighting style back to SFC 2/OP which IMHO worked best. This also removes some of the issues programming and while playing as you don't have to deal with what someone stated "jumping bean" players.
This way keeps the warp terminology in the Star Trek game while keeping used for what we repeatedly saw on screen... as a way to retreat.