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I would say that in an ideal world, traffic should not be throttled for any reasons. However, I think your scenario totally makes sense. Here is my take on it:

Pretty much any legal torrent content can also be downloaded through HTTP. (The main reason people use torrents for legal traffic is because it is often faster, e.g. when downloading Ubuntu on the day of the release.) So if torrents cause ISPs to have to raise prices, add data caps, etc., then I think it would make sense to throttle torrents to a level that makes their strain on the network equivalent to an HTTP download. This would have the consequence of both discouraging people from using torrents, and increasing HTTP speeds because of the decreased congestion, providing an incentive to use HTTP for legal content.

The true core of net neutrality is what matters most: that ISPs can't discriminate based on content, origin, or destination of traffic. This is the part that will encourage innovation and keep the market open. The other part of net neutrality, that is to not throttle based on protocol, would be nice, but may not be realistic. I think that if people were a little more pragmatic about this, we might end up with a law that will please both the ISPs and the majority of users. (And most of the unhappy users would be pirates.)

I should note that when I say that ISPs should be able to throttle based on protocol, that is only for protocols that inherently cause congestion, i.e. P2P protocols. ISPs should not be able to throttle Google's SPDY in favor of HTTP, because they are similar in the type of traffic that they provide.