The only way to patch this game so far is by hacking it. So a good anti-virus treats this as a potential threat that could be trying to hack your system.
An alternative to this false-positive would be to provide game files that has already been patched. The problem with this approach is that my multiplayer mod will probably require this same hacking techinique to work in the future, and players would lose the ability to undo (unhack) specific mods they wish to turn off.
I'll see what I can do to workaround this.