So far I understood that Microsoft is paying Novell in exchange for a joint patent agreement on Office products. Software patents are indeed evil, but I fail to see what's so special in this case. Novell also agreed to improve interoperability with MS Office by including OpenXML/ODF translator in OpenOffice, which seems perfectly normal - many OSS projects are sponsored by corporations, and sponsors naturally have a say in what features get implemented.
Finally, I don't understand how these issues (if I correctly understood what the issues are) are addressed by this GPLv3 clause quoted by Wikipedia:
You may not convey a covered work if you are a party to an arrangement with a third party that is in the business of distributing software, under which you make payment to the third party based on the extent of your activity of conveying the work, and under which the third party grants, to any of the parties who would receive the covered work from you, a discriminatory patent license [...]
What is this "discriminatory patent license" and who will receive it?