He's a really complicated character with a complicated past. If you think about it, Obi-Wan was just as responsible for his demise as Palpatine. He was supposed to be his Master, but he left Anakin to fend for himself and was even against training him.

And like you said, the Empire was at war with the Republic. A lot of times it's easy to forget that even during war there are casualties and aggressors on both sides. Soldiers and generals choose sides and hope they win because otherwise, it's the other side who will write history.