One thing I'd really like to see in Conan to differentiate it from other survival games is to split the PvP design goals to reward gameplay that's more fun and less trollish. This also works from a realism standpoint. I think PvP has three goals: stealing (raiding), war (destruction), real estate reclaiming (total destruction). These objectives should have entirely different tools and rewards.
Stealing – I think the most frequent objective of PvP in these games is for people to rob each other. The best way to accomplish this is door breakers and lockpicks. This way the people getting robbed have a minimal amount of rebuilding and wasted effort and the people robbing get an easier way to get stuff without being jerks about it. Destroying objects should also destroy a decent amount of the stuff inside to discourage blatant vandalism. This also works from a realism perspective, if you wanted to steal stuff you'd break down the door and just grab it. As others have suggested, you should also be able to surrender and offer a payment to be left alone.
Clan war – sometimes you need to destroy your enemies. This should be allowed but resource intensive. You should need a bunch of people to pool resources to build the siege weapons to humiliate your rivals. Here it's about sending a message, and the effort and rewards should align with that goal. Primarily, most of the stuff should be destroyed when playing like this so the reward should come from bathing in the rubble of your enemies. It would also be good end goal for clan warfare for one clan to offer the other clan a tribute to end hostilities and surrender. It would also be good to do as suggested and have structures only destructible during certain server set time periods, to encourage actual warfare and not just waiting until no one is around and playing single player "I destroy stuff."
Real estate reclaiming – The more popular the server the more it's going to be littered with junk builds and abandoned bases. Unlike in clan warfare, cleaning up this trash should not be difficult and should be rewarded. I suggest having any structure unused for x time become abandoned and any player can whack it to reclaim 50-75% of the materials.
Basically, I think these design goals should be split to not discourage people to build cool things but also not make it risk free. Players should be able to specifically do the thing they want to do without causing unnecessary destruction. Factional warfare should be encouraged within fair parameters.
I also think that, to the extent possible, players (not admins) should have the tools to enforce rules over having them hard coded into the game. For example, if a clan offers peace for x time and then breaks the peace then that clan should be marked in game as dishonest rather than just not letting them break the peace in the first place. Same with players excepting a surrender and then killing the player.