One of my kids attended a classical-ish Christian school for a while (until we had to move out of town). That school had some Wilson-connected materials, but wasn't "FV" at all.
Wilson is a big player in classical Christian education, and a bright one. So his work is bound to come up in some materials. I wouldn't worry too much about that making it FV unless the materials he's edited deal directly with the study of the church, or justification, or something else you might find controversial. If this is something that concerns you, I think what you really need to do is find out as much as you can about the school. What is its philosophy? Who are its leaders reading?
They should also give you a chance to take home some of those materials and look through them. My guess is the FV distinctives won't show up in the materials, but you never know. And even if the leadership of the school is FV oriented, from what I've seen of the movement they may not tend to use the school to indoctrinate kids in religious matters to the extent that, say, a Catholic school probably would. Ask about that.
A classical Christian education can be a very good thing for some kids. The fact that Wilson recognizes this, and has made notable contributions to the field, should not cause us to reject an otherwise good thing just because he's associated himself with it. So you're just going to have to be an involved dad (it sounds like you already are), have those talks with folks at the school, and find out what you really need to be concerned about and what you don't.
---------- Post added at 04:28 PM ---------- Previous post was at 04:15 PM ----------
One more thing, in case the school is FV-friendly...
Depending on how they conduct themselves, and the other choices available, I don't know that this would necessarily be a deal-breaker for me. Would a public school or a evangelical-lite sort of "Christian" school be better? The FV movement has problems to be sure, but generally speaking, how they educate their kids is not one of them.