We have left over desert pie crust. Can we use it to make butternut squash onion and goat cheese pie?

Why not? The tang of the goat cheese should offset any sweetness in the crust, and the squash and onions are both a little sweet too, so a sweetish crust makes sense.

I think that would be fine, especially since you have some sweet flavors in the savory pie -- you could also sprinkle a little salt or grated hard cheese like parmesan on it when you roll it out to balance things out.