It's fine as a recurring theme, as I mentioned above, my only contention here is that I don't think our wonderful story team are going to be giving us villains like this often.
What you mentioned, assuming that's the route they're going with, will help flesh out mechagnomes as a proper Allied Race, and give them a reason to exist (unlike, say, LF Draenei). I'm not sure I'll be over the moon with them, but it's also not my faction.