Someone can be a significant contributor but still not be a founder. My wife and I agreed not to list her as a founder on my YC app even though her contribution has been significant. If I walked away from ourdoings.com, she probably wouldn't find another coder to make it happen. If she stopped contributing I would still make it happen.
You could have said that she's a founder as well. I think that could have even increased your chances of being accepted. And if you say she contributed enough for it to count, and you know that both of you would quit your jobs to work on the idea if you received a lot of funding, how does that not make her a founder? You as a family would also keep more of a company as two founders than as one, if you had to give stock to your first or second employees who join later on (I could be wrong.)
The initial team who implemented it and brought the idea to reality/first prototype?
First X 'employees'?