They either continue to use their fork and call it something other than wordpress, or they use an unmodified version of wordpress and are permitted to call it "wordpress", or they pay for rights to use the mark for their modified version.

No doubt this has all stemmed from the issue of them taking and not giving back. If they aren't going to play nicely and pay proportionally for development as per the pledges, then they can pay for the right to use the mark for their fork. Why should automattic and dozens of others pledge thousands of hours of dev time per week when one of the biggest users pledges 40 hours? It may be permitted as per the GPL, but use of the mark is subject to fair use - and fair use doesn't cover them passing off a fork of wordpress as wordpress. Clearly that technicality is being used to force them to pay their share through licensing of the mark.