Not allowing you to exclude a file from scanning it's a serious limitation, and it's a very well known one of McAfee, and I don't see why it would think it's a "critical system file", considering it's not installed in any of the system Windows folders.
The only suggestion is either turn it off entirely, or switch to a more reliable product, like the free MS Security Essentials, which not only doesn't have this limitation and lets you freely exclude any file, but it also doesn't mistakenly block our files, wrongly believing they are threats, so it doesn't even require to exclude anything.
I usually exclude the *whole* FS9/FSX folder with MSSE, not because it's required to run our software (MSSE doesn't have this issue), but just so Flightsim will then load faster.