If you read the war of the ancients, Illidan wasn't just imprisoned for that, but also for (attempted?) murder when he attacked those that tried to stop him, it's been a while so I forget if he actually killed anyone. That brings another moral quandry though. Is life imprisonment morally acceptable when you're immortal?
What people seem to overlook is that the high elves DID NOT KNOW they were building on a troll burial site, at least not until the trolls started the war. They had just come to the EK and just fled the place driving some of them crazy. They found a good place and started settling without knowing where they were. It's not like they just decided 'eh, let's desecrate this burial site because we hate trolls.'