I believe most ISPs don't care if the file you download is "good" or "bad". What they probably do, and IMHO should care about, is prioritizing interactive applications over bulk downloads.

Anyone with the "all data is the same!" mindset hasn't worked in a carrier-scale network. QoS with packet prioritization is an absolute must from an ops standpoint; otherwise your DNS queries would be prioritized at the same rate as someone streaming Netflix. Drop Netflix packets and the video quality degrades a little; drop DNS packets and you effectively have a total outage and customers are burning up your phone lines. DNS and SYN/ACK are probably the highest priority, but there are other tiers for things like VoIP, online games, etc. that have good reasons to go above "bulk" traffic.

It's more about latency sensitivity than anything; but with asymmetric connections (which many ISPs, particularly cable, are forced into for very good technical reasons) Torrents in particular can have a disproportionate impact on available upstream bandwidth. For that reason, most ISPs will crush Torrent downstream to limit upstream data rates (which they can't QoS as easily). I can't say it's the wrong call; and it has nothing to do with the legality of whatever people are downloading.