Q: Delete or permanently disable iMessage

You and your wife should each have your own AppleID's.  You can change your password to your apple ID, which will prevent her from authenticating and logging in using the same ID until she has the password.  Then create an ID for her to get her out of your account.

There is no way for you to remotely do anything other than changing the password.

All you can do is turn off iMessage on her phone, there's no way to delete it.

get separate appleID it's like a social security number sharing it is a bad idea

apart from the call log you also can't iMessage or facetime each other when you use the same appleID

if you do it just to share purchased apps then you can do that using family sharing Family Sharing - Apple Support