Erk :/
I'm sorry guys, but I managed just a few minutes (several restarts; one system backup restore later) to fix both Sniper Elite and Spotter.
Unfortunately I still haven't found an easier way, asides manually removing registry keys, to get rid of the multiple entries in command panel>uninstall but I did manage to get past the 'malware'.
I haven't found a good fix for this (beyond buying Steam version, but that requires more hassle to work without Steam) online or talking to anyone, so I thought I'd post it here since this forum is quite high on the google searches for anything "sniper+elite".
Windows 7 seems to think - possibly due to the alteration of a dll file in the windows/sys directory - that the Starforce Disc Protection is invasive malware. Such, it will restore itself to a previous state (possibly a while ago) and remove a lot of .exe's and other files to, i suppose, insure that there can be no spread.
A bit like burning down next door's house, so that the whole street doesn't catch fire maybe...
You don't need to execute autoplay or setup.exe, from the disc, in compatibility mode as it installs fine; the game does not require compatibility either.
What does need attention is the protect.exe that is present once the game is installed.
I believe that there was a similar - easier fix - for Vista and/or Win7x32 (I must use x64), so this fix is based on that.
The protection exe will attempt to remain resident in memory as to complete its installation on the next restart, so that when windows shuts it says, "i'll open this next time I start, only I think it's a virus, so I'd better fix it and screw up a load of stuff while I'm at it".
It doesn't need fixing...
It [the DRM, ie starforce] just needs circumventing.
Idk if I should talk to much about that here, but you will find it if you have a pair of sharp scissors at home (cryptic). Or whatever...
It can be done a numbe of ways, but the easiest is to just use whatever's lying around.
As I've been told off for posting too much/long in the past, I think I'd better shut up now

Just thought it'd be good to have a small hint of a way to get Sniper Elite (disc version, 1995) to work on Win7x64, as there is no good info on the net.
Another few keywords for Gentlemen of the Scope.

Take care,
Sara