Look, as much as I don't like it, this is a tradeoff. On one side, you have the fact that websites like this would normally be liable for everything they publish. DMCA says "we'll fix that for you", the cost being "if you want safe harbor, and someone with a good faith belief sends a takedown notice, you honor it".
If StackExchange really believed the material was non-infringing, they could always ignore the DMCA takedown, and force CipherCloud to sue them. They didn't choose to take that risk. Newspapers have the same issue, FWIW: They get threatened all the time by bad actors (and not just for defamation of public figures, which the are mostly protected from). They just often choose to take the risk and force bad actors to sue them.
It's not at all clear what you think the solution is. If you institute harsh penalties for filing "bad" DMCA requests, all that would happen would be large numbers of lawsuits over DMCA requests, bad or good, because it would likely be profitable. You really think torrentfreak/isohunt/et al wouldn't just start filing suits over every single DMCA request they receive? What do they have to lose? They wouldn't have to win many suits to make money off it.
If you have a good solution, i'd love to hear it :)
I realize how odd this sounds, and i really do hate the way content companies/et al abuse the DMCA process, but one doesn't need to look very hard at history to see what lawyers in general will do if you make it profitable (see the history of rule 11 sanctions, particularly, the period from 1983 to 1993, or you know, recent prop 65 litigation, resulting in everything in the world having "the state of California believes this may cause cancer" labels on it ).