This year's #6 seeds were right in the mix all along, so the league would have nothing to be embarrassed about if they played each other in the Super Bowl. The Seahawks, on the other hand, would've made some people uncomfortable. It's really best that they got blown out today rather than in a later round.
I'm pretty sure that we've never had two wild card teams in the Super Bowl. But here is the list of wild card teams that have won it:
1980 Oakland Raiders-Super Bowl XV (played in 1981)
1997 Denver Broncos-Super Bowl XXXII (played in 1998)
2000 Baltimore Ravens-Super Bowl XXXV (played in 2001)
2005 Pittsburgh Steelers-Super Bowl XL (played in 2006)
2007 New York Giants-Super Bowl XLII (played in 2008)