I guess you are right about moving it to another folder or directory other than the Program Files (86x) folder. But then it can probably have consequences like you said, there's a critical reason why Windows put installed programs into that folder or the other if the systems architecture is 64bit. But you might wanna try installing your specific program into another folder or better yet a different drive letter. I've tried installing DreamMail email client into D:\programs and it worked well without problems, but then again there's a possibility that it might not be applicable to certain programs.
As far I know, you can choose to custom install your program into a folder/directory/path as most installation wizards I've came across always provided an option/step to browse where one prefer the program to be installed into.
But then again, like I said earlier, I am not that confident or have enough knowledge when it comes to this kind of issue, so whatever you decided to do or opt for, please post back your result so we can try whatever it is we must.
Good luck and God bless,
