I know the pain....
I used to practice Kendo in a Dojo where the floor was concrete with a thin layer of vinyl on top. No mats that is. It was pretty tough on the knees.
Unfortunately out instructor would'nt accept anybody not sitting i Seiza, so we had our share of pain. He liked to talk for a long time as well - so sometimes when it was time for us to stand up and practice we looked like a bunch of old folks that couldn't find their canes.
Anyway - my point is: don't worry about not sitting in Seiza. Do it for as long as you can, and then shift position. Don't let the pain keep your attention from what your instructor is telling you. That would be far more insulting than sitting with your legs crossed. Eventually you will build up flexibility in your legs, and you will be able to sit in Seiza for some time, but don't let it bug you. Focus on your Aikido instead.