We have different iCloud account
The problem is that previously (a) the iTunes library presented your music collection (which could contain stuff bought from the iTunes Store, even bought via multiple accounts, as well as ripped CDs or audio files obtained by other means) and (b) each iOS device (or iPod) could contain a subset of that library.
With Apple Music and iCloud Music Library (the former is both the umbrella term as well as all the streaming and discovery elements, and the latter the 'My Music' section once you have iCloud Music Library enabled), the 'library' is centred around an Apple ID for iOS devices. The iTunes library is a hybrid between on one side the conventionally obtained music (iTunes Store purchases, ripped CDs, imported audio files) and the iCloud Music Library linked to the currently logged in Apple ID.
Thus in principle, you simply would have to log out of your Apple ID/iTunes Store account in iTunes and let you wife log in for her account to customise what she wants in her iCloud Music library. While that would give both of you access to all conventionally obtained content, any new content might only get added to whatever Apple ID was logged in at the time it was added to the library (though you can add content without being logged into any account via ripping CDs for example, but music added from the streaming side by one user certainly won't show up in the other account).
While this may allow you to curate your iCloud Music Library content separately, you won't be able to anymore select a subset of your iTunes library to sync to your phone. I would suspect that every song that is made available offline in iTunes gets also to be made available offline on any device linked to the same iCloud Music Library account. Maybe if you uncheck a song in Tunes (that is downloaded) it won't be made available offline on the phone (this works for legacy content, ie, purchased, ripped or otherwise locally imported content), not sure if it works for content only 'rented' from Apple Music.
But the big question is whether switching between two Apple IDs within one iTunes library works smoothly and doesn't mess up things (maybe you would have to go so far as disabling the iCloud Music Library, then log out, followed by logging into the second Apple ID and then re-enable the iCloud Music Library). Maybe this works but with every switch the local library has to be first synced up with the iCloud Music Library which might take a while.
I cannot test things anymore since about half an hour ago iTunes has decided to hang about 10 seconds after launch (it works fine for ten seconds but then beachballs, though the audio keeps playing until the end of the song). This might have been triggered by me enabling iCloud Music Library (though I am 100% sure I had enabled that already two weeks ago but when I checked today this box was unchecked, my fear is that this go unchecked when I logged out of my iTunes Store account). After the enabling it took a few minutes of synching (illustrated by some syncing messages in the top right corner).
EDIT: After about ten force-quits and waiting for a few minutes, the beachball disappeared. I had waited a similar amount of time before without iTunes coming back to life (but then I killed all iTunes processes in Activity Monitor after the seventh or so force-quit and I took all my iOS devices off the network to reduce the amount of distractions for iTunes).
EDIT 2: Logging out of an iTunes Store account in iTunes definitely disables the iCloud Music Library (not a big deal since the synching after reenabling it following logging in to the previous Apple ID seems to be fairly quick, but still annoying since I need to log into my second account to update the apps bought with the second account and I sometimes switch accounts to get content not available or being cheaper in one of the accounts as they represent two different countries in my case).