Virus scanning was added to Chrome a year ago, but it seems a recent update has some very aggressive virus signatures and heuristics.. Apparently the 2600 Halo rom also has malware!
There are instructions in that thread on how to disable the check globally, if you so wish. I really don't think stella has a virus, and there's not much to be done here. Unlike other AV vendors, Google doesn't have a process to appeal and white-list a falsely flagged executable.
The executables from my open source projects, which are cross compiled on Linux and never touch a windows box, are regularly flagged as containing viruses, though the vendors always disagree on what. They use heuristics like "small download" and "not signed by a developer certificate" ($$$), in addition to overly-small overly-generic signatures that get triggered by a Hello World test.