It happened in HF, it's not difficult to make it happen here. He just has to stumble on a bit of information.
And, yes, of course I intend to follow that path, because that is why I want to play the game. Milbunk has made it quite clear that we're allowed to play our characters as we wish, that includes Shirou being a little more Sakuraphilic than in canon.
And, Zouken is genuinely crazy. He doesn't even remember why he is fighting for the Grail. He's still capable of reasoning, yes, but I don't think he's quite as competent as people make out. Certainly he tends to over-estimate how much control he has over things.
Also, I don't think Zouken would kill Sakura out of revenge, not unless he was dead anyway. His sole desire is to survive, Sakura means nothing to him.