Well, I never thought of it hurting my HE washer and so far, so good. I've used vinegar for a couple of years instead of fabric softener and to keep towels fresh and if it's hurt the machine I can't tell.
I have used it too, though I just got my machine not too long ago and still no problems. I can't imagine vinegar harming the machine. What you can do is use 1/4 cup instead of the recommended 1/2 cup (that's what i do) just to be on the safe side. With those machines you seem to need less of everything! :)