What the heck was Luke supposed to do, whip out the lightsaber and go to town on them? (BTW, I don't even think he force-choked them; it always looked more to me like he put them to sleep.)
This is the problem I've always had with Jedis - you can stand on your head and see visions or move some boxes around with your mind, but try to get anything positive done with your powers and you're "skirting the Dark Side". You can feel free to chop up all the cannon fodder henchman you want with your fancypants laser sword (just watch the scene on the barge later - Luke throws down big time), just don't wave your hand in front of them and tell them to take a hike. And Yoda will pitch an adobrably mangled hissy fit if you force-choke them, even though the net result is still dead cannon fodder.