We still all remember the Tractor Beam Mines, do we? That's the kind of nerf these Runabouts probably need. They get their own Tractor Beam, and it will be considerably weaker than a player Tractor Beam. Then, 4 Runabouts grabbing you may stop you like a fully fledged Tractor Beam 1. That's probably okay. As long as a single POlarize Hull or Attack Pattern Omega can clear you from any number of Tractor Beams. (not just 1, not just 2, not just 4, any number.)
I think the simplest and most likely to work solution is this:
1) Invent Time Machine
2) Travel back in Time before the Startrek Online Beta
3) Capture every Cryptic Dev and go all Clockwork's Orange on them, but in regards to Carriers, not violence.