Yes, Autofill uses the info in Contacts. I would need a way to specify my wife's contact page as well as mine.
The only solution I can think of is using a third party Safari extension such as
Text Templates For Safari to fill in the forms.
NOTE: I have not personally tested Text Templates For Safari so I offer no assurances that it would work the way it sounds in the App Store description. My wife and I resolved your problem by each of us having our own separate logon account. That is not always ideal either.