Hello Primer Driver,
Thanks for the question, and what a great question it is.
You are absolutely right, there are some tweaks we will want to make to continue the configuration you have right now. My recommendation? Create a new Apple ID for your Wife, but only use this Apple ID for iMessage/FaceTime.
There are four different accounts you can be signed into on an iOS device: iCloud, iMessage, FaceTime, and iTunes and App Stores. Theoretically, you could be signed into four separate accounts for each of these. For your situation, your Wife would only sign into iMessage and FaceTime with her account, and continue to use the family account for iTunes and App Stores.
For information, see these articles: