Erroneous "Installation Alert" upon installing Xcode 3.2.6
OK, I solved it. So I first found this article, which said to killall iTunesHelper. That didn't work. After that I found an Apple discussions thread on this where someone had to killall AlertAll (the process responsible for the Install Alert). I did that and the installation finished succesfully.
Step-by-step

Go through the installation and get this alert
Open Terminal and execute killall iTunesHelper (or kill it with Activity Monitor)
Execute killall AlertAll if the installation still doesn't proceed (Caution: after this the installer assumes iTunes is completely stopped. If it's not, things can of course go wrong. So better look over your processes list twice before doing this.)
Everything should be fine

This was exactly what I did, if it doesn't work for you: I'm sorry, but then your issue is different and you should ask a new question.