I had the flash forward pegged in the first flashback, too. The "go get my dad" scene didn't really throw me, because the new chief of surgery looked at him like he was insane to suggest that. It was just more proof that he really had lost touch with reality.Throughout the episode I just kept thinking "there's no way this fits into his timeline if it's pre-crash". There simply wasn't enough time for him to have gotten divorced, gone to Thailand, come back, gone through chemical dependency, gotten clean enough to get re-hired at the hospital, ratted out his dad, and then gone to Australia. It just doesn't fit.
Then again, Jack Bauer kicked heroin in about 4 hours, so I suppose it is possible. /sarcasm
As for Locke, it totally makes sense to me. Locke is on a path *forward*. His whole agenda is staying on the island and serving the island. Naomi threatens that. Therefore, she must be stopped by any means necessary. It's why he tried to kill Mikhail. It's why he clubbed Sayid. As much as he hates his dad. He represents the past. Killing him would simply be revenge. Revenge doesn't fuel him. The island does. I think the only reason he didn't shoot Jack was because if he had, he would've had a full scale riot on his hands and wouldn't have escaped with his life. He did the best he could there. He bluffed. Jack called it and won.