No, not really. They didn't pay for any software at all; that's the whole problem. They paid for a service. If they paid for some software, they could just stick with what they have instead of pissing off users by divulging their identities when the users had never agreed to that before, at least until they could get the software made so that old comments used the pseudonyms while newer comments switched to the new policy.
Instead, they bought a service which apparently doesn't offer this ability. I don't know if there's a legal case to be made here, but it seems to me that their website had a policy before where people could make posts anonymously (or pseudonymously), and now they're changing to a real-name policy. That would be OK, except they're making it retroactive, which is certainly wrong ethically, and quite possibly legally, depending on the wording of their prior user agreement policy. You can't just go change agreements like that retroactively. And the fact that the SaaS vendor doesn't support this is no excuse. Either they need to switch to a new vendor, get the vendor to change, or eliminate the service (and comment section) altogether.