I think it depends on HOW we get left out.
A few scenarios:
1. Iowa wins out but never climbs higher than 3rd in the BCS rankings because the SEC champ and Texas both finish unbeaten.
Fallout - moderate. We'll be like Auburn in 2004 - a 3rd unbeaten contender wishing there was a playoff.
2. Iowa wins out but never reaches #2 (or higher) because they were jumped over by a 1-loss team (USC, Miami, etc.).
Fallout - high. Iowa's schedule difficulty should avoid this, but "name brand" schools often get preferential treatment by voters.
3. Iowa wins out and finishes #2, but then watches another team jump them during conference championship weekend.
Fallout - catastrophic. This scenario is bound to happen to some poor Big Ten or Pac Ten school because they choose to end their seasons in November. The public meltdown that occurs in this scenario will be something to behold.