No question that it will hurt their chances. And I don't think the NCAA will allow Big 12(-2) a conference championship game, if they were to appeal that ruling and get a exception.
Their AQ status will not come into question. The teams in the B12-2 south are more than enough to keep their AQ status. Sure the conference is weakened but not so much so that it becomes a WAC or MWC. I think it will fold due to more greed by UT, but not because of a lack of AQ status. This league is set up perfectly for UT and OU to rule it. They are basically garaunteed 10-12 wins every single year.
I don't know...if you take a step back it doesn't look that different than the MWC next year with TCU and Boise at the top.