Zouken can out plan pretty much anybody, and would guaranteed have back up and contingency plans waiting.
Thinking Sakura attacking him wouldn't be covered in one of them, is being entirely biased, and ignoring Zouken's abilities in canon.
Zouken is a pretty damn good planner, yes, but he has the fatal flaw of underestimating the mental strength of others, especially people who are under his control. That's what killed him in HF, ultimately, and that's what allowed Sakura to surprise him here.
Plus, what could he have done? Even if he'd somehow gotten hold of her, Archer would have rescued her, and probably killed him in the process. He could have outright killed her, perhaps, but how would that have helped him?
The only thing that gives Archer an edge, is he's from the future, and you're still ignoring his probable back up plans to get Sakura, or simply find another host.