You can't do that without messing up the AI to the point of it being incapable of playing the game. The AI relies on specific ship types to be available, such as siege frigates, scouts and colony ships. Without them its very likely it would just sit there.

What you can do is make every frigate a sort of a peudo-capital ship - change its mesh reference in the entity files so that it looks like a capital ship, and its stats so that its as strong as one, but leave everything else. This will in some cases also require you to add/remove certain hardpoints from the mesh files.