Yes it is sad but true. You will now have to wait 90 days until the computer can be authorised in your account again.
If you go to iTunes Store, log in, go to Account (under your name) you will need to log in again. Click View Account, go to Manage Devices under iTunes in the Cloud and you will see your computer has a day countdown next to it and if I remember correctly a link to a page which explains why.
We have many queries about this issue. I believe it is because people think iTunes is like a website. It isn't. It is a native application intrinsically linked to your Apple ID, the iCloud and your computer registration with Apple not to mention your Apple user profile. This also applies to iChat, FaceTime and Find My iPhone. They all utilise unique device identifiers registered under your Apple ID.
Putting all Apple services and devices under one ID is convenient and improves security on the one hand but makes sharing difficult if not impossible. Your wife could have setup an Apple ID and profile using her iPhone only but doing that on your computer prevents her (or anyone else) from stealing your paid for Apps and Media.
So your computer remains associated with your account but becomes "Unauthorised" for your purchases for 90 days. Sorry there is really no way around this.
These days an iPhone is really a stand alone device requiring connection to iTunes only for backups or restore.