Nothing will let you merge AppleIDs. It's the way things are set up.
If you don't like iTunes, don't use it. With Lion it is built into the operating system so you can't delete it (I don't think). You can re-assign things to open with other applications.
Mac OS X: Double-Clicking a File Opens the Wrong Application - http://support.apple.com/kb/TS2291
-= Changing the application used to open all files of a certain kind (written with reference to OSX 10.4 but may not have changed) =-
1) In a Finder window highlight a file of the kind you want to change the application to open that kind of file.
2) While that file is highlighted, select File > Get Info or press command (apple or propeller icon) + i to get a file information window.
3) In the lower part of the info window there is an "open with" menu with a list of applications.
4) If your application is already in the box then it is the default application for opening that kind of file and you don't need to do anything more. Close the get info window.
5) If the application showing in the menu is not the one with which you wish to open the file then select a new application. If your application does not appear there then select the "other..." and track down the application (usually in the Applications folder at the main level of the computer).
6) If you wish to change all files of this type to open with this application in future, make sure the "change all" button is selected.
7) Close the get info window.