I have a theory as to why Dogen didn't kill Sayid when he had the chance, what we are possibly seeing in the sideways flashes, Jacob's and Flocke's agenda, and why Sayid couldn't kill FLocke. I hope you enjoy it.
In the first on island scene in the episode Sundown we see Sayid and Dogen go at it. The scene ends with Dogen pinning Sayid and holding a knife to his throat about to kill him when his baseball drops to the ground. He hears this and has a change of heart in regards to cutting Sayid's throat. He tells him to go, leave this place and never come back. Why not just kill him if he really believed he was better off dead? Which we now know to be true considering Dogen was drown at the hands of Sayid. I think Karmic lessons play into this show in some way, and what we are seeing in the sideway flashes are the result of the choices of the losties in the original (island) timeline. This explains why Dogen didn't kill Sayid for he knew about the ramifications of that action on his son, where ever he may be. The baseball reminded him of his son; we learned this from his conversation with Sayid regarding his back story. I think we will soon find out that all those who choose to be good/! light will have some sort of resolve in the sideways flashes and those who choose to be evil/dark will be doomed to play the game again eventually finding their way back to the island. In regards to Jacob and FLocke, Jacob is trying to prove that man can find his way to redemption on faith alone and is innately good. FLocke on the other hand is convinced man is innately evil, will always falter at temptation and will ultimately kill for what he wants. Also one more thing I wanted to touch on was why Sayid couldn't kill FLocke. I think the reason that Sayid couldn't kill FLocke is because he was not completely aligned with him yet. Let me explain, the reason Jacob could be killed by Ben was because Ben had full allegiance to Jacob's will. Only when a person committed to one side either dark or light turns on the embodiment of their own side, Jacob or MIB/FLocke, can the leader be killed. Sayid truthfully still had good in him, rendering his attack useless. Only when Jacob or! MIB/FLocke are betrayed by one of their own "pieces" can they! be kill ed.
I don't know all the details, or it wouldn't be LOST. Just a few ideas.
P.S. - If you need even more proof regarding why Sayid Couldn't kill FLocke look at this dialog between FLocke and Ben in the season premier LAX.
LOCKE: You can stop staring at the fire. Jacob's gone. He's gone.
BEN: Why didn't he fight back? Why did he let me just kill him?
LOCKE: I guess he knew that he was beaten.
Thanks for reading and be kind :)