Well, it's not that Zouken wouldn't allow it, it's that he'd expect her to still go all-out to win the war. Which means that he'd expect her to backstab Shirou when it was convenient to do so. In HF, Shirou is already out of the war by that time, so it's not an issue (and Sakura expected she would probably have to fight Rin eventually), whereas here he's not. Plus, in HF Zouken is obviously the enemy for Shirou and Rin, so Sakura expects them to try to take him on (and, thus, bypass this issue), whereas here he's not even mentioned as far as I can tell.
It's not impossible for it to happen, but the danger for Sakura is that she would be forced into backstabbing Shirou, so she would probably avoid any kind of formal alliance. She would, however, probably assist him if he was in danger.