I find Cody's loyalty very conflicting. If your read up he's one of the trained Commanders of Alpha-17, free will thinker so to speak. I think in circumstances based upon his training and such, him issuing Order 66 is not a part of who he is. Nor is it something I find he wanted to do, that's the thing about helmets; no expression. From the comics and such Cody was Obi-Wan's right hand man and friend. I find it hard to consider that making him out to do Sidious' order was to his liking due to the fact regardless if he carried it out he'd be killed for treason. Cody was always a rule-by-rule clone however and I think in the long run, Obi-Wan held no grudge. He did what he was told to do like he'd done all his life.