With a few exceptions...like some antivirus programs and probably others I can't think of at the moment...no, disabling them from loading on startup doesn't affect their functionality when run.
I have a couple of programs that wanted to load on startup when I installed them, I disabled that and when I open them, they work without any problems. However, I've never used Media Center or iTunes so I can't adivse you on thier specific problems.
You may find that getting the Services sorted out properly with the help of Black Viper's site fixes some, maybe even all, of the locking-up problems you're having.
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