I'd probably get some boots and go. Acqua alta is fairly common in Venice. People put on boots, in some places they drop some platforms for people to walk across, and life goes on.
Plus, the prospect of acqua alta might scare some people away, and a less crowded Venice is a rare and wonderful thing.
I really didn't like Venice the first time I visited. It was July, it was full of people, all tourists, like a giant cruise ship terminal. It turned out I was doing it wrong - I needed to get away from Rialto and the city was completely different. The locals I then found told me to come back in the late fall or winter, maybe get lucky (yes lucky!) and find acqua alta, and have the city without most of the tourists. Then it'd be even better.