I feel like the only person who is "hurt" by (good) live versions is the singer, so the fidelity of the vocal track is pretty important to consider. Maybe if you're charting the vocals, make the really deviant lines into talkies, or make them more forgiving, so that people won't be penalized as much for only knowing the original? Don't know if that would work in reality, but it's a thought. For the rest of the instruments, note-for-note familiarity really isn't much of an issue, as long as the song still sounds great and is fun to play.
But yeah, the idea that Harmonix could theoretically someday get the original masters is pretty irrelevant in the grand scheme of things.