I agree with you that the capture ability is somewhat overpowered. However, I did some experimenting with it in a single era GC, and notice a couple of things.
First, the ability can be used 4 times in a battle. If you are in a battle large enough to utilize all of those attempts, I can guarantee that you will lose at least half of what you capture as the faction you are fighting will attempt to destroy those ships. I would cap it at 3 uses per battle because the capture method is VERY imprecise to start with. More often then not, my capitals would destroy the ship before the shuttles can take it.
Second, as far as old canon goes, which the staff try to stick to as much as possible, making capitals non-capturable would break their dedication to canon. Even in new canon the rebels use boarding parties to take Star Destroyers.
As far as nerfing the ability further, I would make them an era specific technology, only available for eras 1-3 for the New Republic, as capturing ships became less and less common for them to do (iirc). I would give the imperials the ability in Era 4 and 5