Well, Harry didn't become Warden of Demonreach until Turn Coat, and that's what moved him from being a potential local-scale threat to a potential world-scale threat.
Early on, if Harry had gone full Dark Side, he'd have been a dangerous and powerful warlock but not as powerful as, say, Grevane or Corpsetaker. And early on, he was being watched closely enough that Morgan would have had a chance to take him down before he could do large-scale damage. So it wasn't worth angering Eb to try to kill him (directly; Morgan did try to goad him into a fight in SK).
But being Warden of Demonreach elevates him to a potential worse-than-Kemmler threat. If Harry wanted to, there's a pretty good chance he could destroy the entire White Council (extract a binding oath from some Mab-level entity to do it in exchange for being released).