Firstly, it was believed to be a "holonovel" when it was discovered. And, when Tuvok admitted what it was, he also stated unequivocally that he had long since declared it irrelevant and erased it. Maybe if Chakotay had discovered it while Tuvok was still working on it, he would have been upset. But this was years after the fact, and Tuvok had not only erased the program, but was the main advocate for its permanent deletion. Whatever Tuvok's reasons for creating it, they clearly no longer existed.
But that's not actually an improvement. Someone writing a holonovel that presents a certain portion of the crew as mutineers is still pretty insulting, no matter what their intent was.
By the time we got Tuvok's current take on the scenario, the crew had already been "playing" for quite a while. It didn't bother anybody before they got this explanation? It must not have; even Torres was okay with seeing her old pal presented as the lead mutineer.
My second-favorite ep actually makes one of these lists and then gets voted off immediately because Tuvok something or other . . . ah, well. Glad I didn't get *too* excited. 
