There's no virus
Some antivirus software detects AutoHotKey scripts as viruses because of the way they work, but if you submit the file to your antivirus vendor for analysis they'll confirm that it's a false positive. You can just add the file or the directory in which it resides to your antivirus software's exclusions list.
You can also look through the AutoHotKey script file for any signs of virus like behaviour, and if you're satisfied that it's clean you can compile it into an .exe yourself using AutoHotKey. It will show up as a virus again, thus proving the original .exe was clean all along.