You are IMO taking that quote of context..
"If you're not with me, you're my enemy."
Thats the absolute, black and white. Right and wrong nothing more.
Jedi tend to realise that there are grays out there, they don't kill everybody that doesn't agree with them. They don't rage wars to spread their idea's across the galaxy just to defend their goals. Thats the absolute here.. With me or against me, just black and white no grey.
Obi was right when he said that, because Jedi don't think like that. Of course they are against their enemy they are the enemy, but unlike the Sith they are not against the guy on the street that doesn't take sides. They would never kill them, Sith would.