There's a part in the GPL that says you're free to discard any terms other than the GPL and specific ones (like attribution). So if they really did apply the GPL, you can use it commercially, but only under GPL terms.

I don't think it's that bad. Most commercial enterprises don't want their commercial products to be under GPL terms, so they'll pay for the license regardless. You should really fix the SaaS loophole by using AGPL instead though.