There shouldn't be any problem for an Administrator to amend permissions on program file folders, i.e. by giving 'write' permission (but you must usually give 'full access' to the shortcut that runs the program as well).
What is often a problem is that on PC's where 'normal' users have limited privileges, it means that an Administrator has to carry out the install. Unfortunately this usually means that the installer creates the application settings folder in the Administrator's profile (e.g. C:\Documents and Settings\Administrator\Application Data\...), not the profile of the user who is going to be using the program.
This is often the case with specialist assistive software, e.g. Dragon NaturallySpeaking, Jaws, Read and Write, etc. What's worked for me is to add the user to the Adminstrators group temporarily to install the program then to remove them from the group afterwards.
This overcomes the problem of the correct profile being amended but still means that desktop and Start menu shortcuts, program file folders and sometimes registry settings all have to have their permissions amended.
If the program uses speech then you have to jump through a few more hoops as well. It can be a real pain... but in my opinion is still better than letting users have admin rights as a matter of course.
Hope this helps...