They could simply send out a few million or so letters, maybe costing a million £ or so. Offer everyone a settlement of a few hundred £ to cover all past transgressions with the threat of suing for a much greater sum if there is a repeat offence or if they do not comply.
If you work on the basis that about 50% just pay up straight away that's quite a lot of money. This money can be used to subsidize going thermonuclear on at least a few thousand of those who don't.
Besides, they don't need to sue everyone to make people scared enough to avoid pirate sites.
Don't forget all (well nearly all) Bit Torrent downloaders are also (by default) uploaders - seeding back to the pool while their file downloads.
MAFIAA and others don't care about downloaders (as yet I don't believe a single user who downloads only, has been sued successfully), but they DO care about those sharing their material. The fines levied so far are not for downloading tracks, but for sharing them.
The key word in the article is "popular" content. It is well known that (a) relatively new and (b) relatively mainstream + popular content (especially movies) is heavily monitored.
The article title is misleading. They logged only popular, public torrent content. I'm certain that many, many other file sharers were not even seen by their study. It's all just scare tactics.