It's been done few times already, there's a lua script that gives the player controle over their turret's targets. It's usually used in conjunction with some sorts of special abilities activated using multiplayer keys (alt+x, 1, 2, 3, 4), and changing how the ship perform when manipulating the energy transfer system (more power to guns = fire faster, things like that).
It's not on the level of say, Nexus, Bridge Commander, Klingon Academy, or even Homeworld, given that you basically need to hammer the engine into submission, but it is doable with a bit of work to make it fun.
There's also a RTS script framework lying around, although as far as I know, it hasn't been used in any released campaign yet.