While Microsoft generally recommends making a backup before making registry changes, in this case, it's especially well advised. Also, while I have tested this, if it makes the ice cream in your freezer melt, your sink to back up, your hair fall out, or anything else bad happen, it's not my fault. I can't promise that there won't be any unintended side effects.
Now, all of that said, the first step will to back up some keys. Open a command window, and issue the following commands:
reg export "HKCR\iTunes.itms" 1.reg
reg export "HKCR\iTunes.AssocProtocol.itmss" 2.reg
reg export "HKCR\iTunes.AssocProtocol.itms" 3.reg
reg export "HKCR\itmss" 4.reg
reg export "HKCR\itms" 5.reg
reg export "HKCR\.itms" 6.reg
reg export "HKCR\MIME\Database\Content Type\application/x-itunes-itms" 7.reg
Now you have backup of the keys. If you ever want to allow IE to open iTunes, you'll need them.
Now, to delete the keys:
reg delete "HKCR\iTunes.itms" /f
reg delete "HKCR\iTunes.AssocProtocol.itmss" /f
reg delete "HKCR\iTunes.AssocProtocol.itms" /f
reg delete "HKCR\itmss" /f
reg delete "HKCR\itms" /f
reg delete "HKCR\.itms" /f
reg delete "HKCR\MIME\Database\Content Type\application/x-itunes-itms" /f
That's it. IE will no longer launch iTunes.
Finally, if you want to put it back like it was, just open your command window, change to the directory where you stashed the registry files, and:
for /l %f in (1,1,7) do @reg import %f.reg
FWIW: I've saved the contents of all of the original keys here.