If you make the INI read only or otherwise restrict access to the file, does the application throw an exception and fail or does it move along and work?
Have you tried to reverse engineer the application? Try to understand why it wants to do what its doing and address it if possible. Perhaps two INI values are mutually exclusive so it decides to correct one of them. Maybe if you correct the other one it won't need to do anything.
Maybe you could grep the EXE for strings and hack it with a Hex editor to get it to write to a different INI file.
Maybe you can reflect/decompile the app and change it.
Really, without knowing what the app is, what it does and why, it's really difficult to try to give you any meaningful assistance.