Well, why would someone want to siege a base when they haven't the means to do it? Some factions simply don't have the power inRP and have to rely on allies. Oh noes, diplomacy. There is pretty much no faction without an ally that can access battleships, so that's a rather moot point.
I strongly recommend to not remove the PoBs, because everyone building one was aware of the danger of it getting destroyed the very moment they placed the base. The problem are not the PoBs, but how people have no loss at failing a siege. Something that can easily avoided by not implementing a dumb second instance like siege platform but by this: Link