Well, the idea for placing it on a dedicated Gravity-Well ship is mainly to prevent abuse, as the idea is it would disrupt thrusters as well. However, ships would still be able to turn and line up their weapons, so anything with a SNAC or two would be able to defend themselves. The things would mainly be used either to 1: blockade trade routes, or 2: equal odds when dealing with large swarms of high speed fighters
Problem is, it would gimp both allied AND hostile ships, so it would be best paired with a Gunboat. Of course, that leads to the problem of potential abuse by a determined capwhore. Though, it's potential for legitimate RP use (Liberator Spam -> RM Gravwell + RH gunboat? Redcats? Etc.) as a tactical asset is solid.
The limiting factor would be the fact that it's on a dedicated vessel, with no other weapons, and it drains both the Energy AND Hull of the ship it's on. So, it's not as simple as letting energy regenerate, you have to worry about hull interigty. And when combatting one, just bring along a gunboat.
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Though, that's really hypothetical. The M-Harpoon may be more practical and less abusable then an area gravity well projector. Beyond it's use as a weapon, it may also be usable by Repair ships or heavy lifters to tow ships and objects around.