PoBs - in their current iteration - are labor-intensive and high maintenance. Thus, players will get cranky when all that time effort gets erased. I don't think it's a Core-Order problem exclusively.
I honestly don't know why people bother building these things. Is it worth the frustration?
If they were easier to construct and maintain, and thus a bit easier to destroy, there might be less ill-will where sieges are concerned.
Incidentally, the Order destroyed a Core base a few weeks ago near Yaren, so I guess karma is catching up to the Order.