This is why you use Omega. You can even run two copies of it. And it gives a damage buff as well as defensive buffs and mobility. I use one omega and one polarize as I feel 4 tactical weapons buffs just brings more to the table with the insane number of opportunities for aoe damage.
Remember everything in the STF happens in exactly the same manner as it did the last time. Just aim the pointy bit of your ship at the bad guys and start pew pewing.
Allow me to explain as that sounds a bit flippant. There's no surprises in an STF. You know where you need your ship to be. It's really just a big game of space turrets. You don't need to out maneuver a borg gate. There are no CC targets in an stf that you can't vaporize, and the targets that you can't vaporize do not move, so they don't really need to be CC'd. Just put you're ship where the bad guys are going to be and blow them up as they appear.