That's not a bad idea for new missions. Maybe give all ships a non-combat version which can only be used out of red alert for towing and such.
They could also upgrade the current tractor beam power. Leave the level 1 version the same, but say level 2 and 3 would have a greater chance of being able to drag an enemy around and cause more damage if you start pulling them in the opposite direction of their facing.
It's true that all ships should have non-combat tractor powers, it's pretty nonsensical that tractor beams, as far as we know, are standard ship equipment but you need specially trained science officers to operate them... if you think about it, this is like needing a special BOFF power to use Full Impulse. Also IIRC it always was ops (e.g. Data) operating them, not Sci
Using them in combat to hinder your enemy can stay the BOFF power it now is, because this is a whole other usage scenario than towing friendlies and such.
On the other hand there's no content to use non-combat tractor beams on. Some good suggestions in this thread already, so far the only solution to "comet!!!" has always been "blow it up!!!".