You can scan offline setup file. Or extract it with innoextractor (with --gog launch argument look to tool's readme).
In extracted files take exefutable and upload it to GirusTotal and force to rescan.
But VirusTotal itself also non-accurate. While it can show treats on result page for some security vendors their offline apps at same time find nothing. Or vise versa.
Few "positive" at result page didnt mean it is real treat.
If AV target at some else files in game or GOGs folder - it kinda normal. There is scripts there to fiddle with Win DISMM service, installing compatibilities as sdb executable packages, enable Legacy DirectPlay and silent updating of VC/DX/etc.
I did install on my In7 every game and very fast-short test it. I disable MSE antiviruss but looks like there is no treats there. Cant guarantee it for 100%. Nothing suspecious happened.