The more I think about the possibility of banning stock weapons, the more I like it. It pushes players out of their comfort zones and encourages exciting, innovative play, which is exactly what Robin and the dev team want out of this. It's the kind of tf2 that I would want to watch. However, this raises the possibility of completely banning out a certain class. This is unreasonable. If the other team has a very strong demoman, we want to be able to restrict him, not take him completely out of the picture.
A simple solution would be to allow only one weapon ban per slot per class. For example, if a team comes up against a strong demoman, they could ban the sticky launcher. This would force the demo to play a more passive, defensive role, but the player will still be a threat (instead of restricting them so comprehensively that they end up playing demoknight). Alternatively, the opposing team could ban the scottish resistance early on, ensuring their best player his strongest weapon.
This approach forces players to adapt and have multiple playstyles at their disposal, while not being able to completely ban out a skilled player.
In terms of the number of total bans or banning order, I'm not sure. I'll leave that question to other better suited to answer.
Overall, I think this would be a simple solution to keeping the tf2 metagame fresh and exciting, and I'm hyped to see what comes out of this.
just my two cents :)