What if they made it so you could use Ender Peals to protect blocks from them moving them? That would give an incentive to kill them and at least give an option to people suffering from Endermen destroying their buildings.
I find it strange that something that is harmed by water is carringing around pearls lol, anyway I think they could be used to strengthen tools. Why do I speculate this? Well Jeb is mentioned here http://www.minecraftwiki.net/wiki/Upcoming_features commenting on how he would like there to be stronger tools but not making them from stronger materials, otherwords using items to add to the current durability. Just my Opinion, thanks!