I actually liked the moral crisis he faced towards the later end of this arc. It had a very DS9 feel to it, where right and wrong become blurred. Sure his actions were morally bankrupt, there's no doubt about that. But it was all for a good reason in his mind. I was hoping they'd explore upon this in season 4, maybe even with Archer temporarily losing his command because of his mindset of the ends justifying the means as he comes to terms with his behavior.