the only problems with bad primaries are problems with primaries who are not patched, as connections to them tend to be... unreliable to say the least
however those primaries also tend to be full of flooders, so a lot of the time clients don't get sent there and you can avoid them most of the time (plus some of the caches check and refuse to send users to unpatched primaries)
is it possible for "them" to set up a primary (or a few) that does that? sure it is possible, is it worth doing? hell no, it would cost a lot in terms of resources, would be extremely easy to block if they did do it (just add them to the block lists) and would have no major effect as few users would be connected through them - plus of course officially they claim to only be attacking piracy so only do things that they can try to justify with that excuse (like attacking users who search for flooded terms - they use the excuse that it is a byproduct of disrupting piracy, or filling secondary slots to try and stop users being able to connect, they claim that as a byproduct of their flooding systems being too aggressive connecting rather than being deliberate)