Huh. That could make for an interesting arc: Shiro trying to figure out how to kill Zouken for good. Something like:
Route 1: When in doubt, superior force is the way to go! Call in sick, get Saber, trace Excalibur and EXCALIBURAAAAAASTOOOOOOOOO the block.
Problem is, three days later Zouken possesses Sakura and returns the favor. DEAD END.
Route 2: Rule Breaker! When overwhelming force fails, smarts and cleverness is the way to go. One little jab and Zouken is done for.
Except, he isn't. Maybe his soul returns to his body, thus alerting him to the fact that someone's on to him. While Shirou's distracted by Sakura's horror that he knows so much about her, Zouken sends more worms to recapture Sakura and eliminate Shirou. The battle goes badly because Shirou has to defend against the worms and keep Sakura safe.
Unfortunately, Shirou sucks at escort missions. BAD END.
Route 3: Gang up on Zouken. Forge an alliance with Kotomine or Illya and go after the bastard. Berserker's ridiculousness means that Zouken will be distracted physically, giving Shirou and whoever he takes with him the chance to nuke the worms.
Problem is, Sakura's still infected. Zouken kills her or hitches a ride on her body soul, thus leading to eventual BAD END.
Or something. >.> Got a suggestion on how to kill him for good?