Alien ruins and other "special" sites need another solution, for sure. Perhaps military presence or similar.
I think Frontier were originally hoping it would happen "organically" with player groups taking the role of defence but this only "sort of" happens. The problem here, IMO, is that the "killers" are specialists who have spent most of not all of their game time practising and engineering towards the one goal of killing players. Whereas the typical defender is a part-time defender who mostly does something else in game, even if that something else is PvE bounty hunting and combat zones they simply don't have the practice or finely engineered ship to compete.
Now, if there was a role for a full time defender/bounty hunter who targeted other players (with equivalent CR rewards to other play styles) then things might get more interesting. Then we might start to see specialists on the defender side too, heck some of the current PKer bunch might even switch sides. For this to happen the rewards need to be there, and the tools to actually do the job (some way to track a commander down, which is still fair and cannot be abused - a very hard problem to solve).
The Gnosis is now up and running. It has a non-anarchy minor faction and therefore should bring C&P to any system it's in (unless it has an anarchy faction already). If you want protection at ruins, you can pick one.