Personally I'm not too worried about this having the affect you describe. Is the length of the ban harsh? I think so, yes. I would rather see it only banned for the next round or two.
The reason I don't think this will be an issue is because of the amount of potential nominees being extremely high, even keeping in mind that there are 9 nominees per round there is a staggering number of choices that could be put up to vote, and having one not receive any vote by someone other than the one that nominated the game is telling enough that there are much better choices out there. The fact that no Final Fantasy game has been brought up, no Doom, no Smash Bros, no a lot of things have been mentioned in the first 2 rounds means there's plenty of games that are worthy and plenty of time to get those that were banned another chance later on.
The "better choices that day" argument I also disagree with because I trust the allies to bring up games that they truly believe in with their vast collective knowledge of games and gaming culture. Maybe my sarcasm detector is malfunctioning, but I don't think that any nominee that we've seen so far has been a troll. A good case has been put up for each game nominated, even for the ones you could call surprise entries like Megaman Legends or Black Flag or Link's Awakening DX.
I guess what I'm trying to get across is this...the chances of a not-worthy game being nominated to begin with and therefore take the spot of one of the greats over a "better" game that was banned previously (and keep in mind, everyone's opinions will differ to a degree as to what game is "better") is extremely unlikely from what I've seen so far, so I both enjoy the added tension it brings and am not worried about another game getting an unfair placement in the HoG.