As far as I see, this is no problem at all as long as you create two independent user accounts on one system, each using a separate AppleId to login to the Cloud and iTunes. I tested it on my Mac (10.8) just now using my work AppleId under a freshly created separate user account and found it to work.

Yes - make one user account for your iTunes library and a second user account for your wife.

As far as I see, this is no problem at all having two independent user accounts on one system, each using a separate Apple ID to login to the Cloud and iTunes. I tested it on my Mac (10.8) just now using my work Apple ID under a freshly created separate user account and found it to work.

This method has worked since OS X was first developed and it's unlikely to change anytime soon. You can search here for other questions that cover how to share some or all of the songs between separate accounts, but it's always easy to combine things later than it is to start mixed and separate things later.