Simple answer: Disable UAC or change the permission setting for the respective program's folder to "Authenticated Users: F, Users: F"
Why you shouldn't do it:
Virtual Store is for compatibilty. I don't believe you when you say "it cannot work if files are not saved in its native folder." Why? Because your program cannot tell the difference between its native folder and Virtual Store. The program sees the files in VirtualStore as if they were in its native Program Files folder. If its a more intrusive program, as if they were in the /Windows folder.
That's the simple answer/s. If you want more detail, see
Windows Vista File and Registry Virtualisation - Richard's Weblog - Site Home - TechNet Blogs New UAC Technologies for Windows Vista
Yes, your registry has a VirtualStore too. Never noticed your program getting bothered with it? Because you probably didn't know it existed.