itunes seems to sync my wife's iphone with  all of MY apps
Anything removed from an iOS device is not removed form iTunes.
Secondly, iTunes sync's all apps that are specified to sync, no matter whose App it is.
iTunes determines the owner to be the Apple ID, which downloaded the App.

Here is an example o the app sync window:


Here you can choose the apps to sync. And remember it will upload apps belonging to either of you, but it won't change ownership of them.