I have no problem with the loser of a conference championship game getting in as long as there isn't a rule against it. Should there be that rule? Different argument.
The top 2 teams in the country could be in the same conference.
The thing is, if the supposed top 2 teams in the country are in the same conference, then they have the chance to solve the issue in the Conference Championship or in a divisional game earlier in the year. What does a rematch decide? Give someone else a chance to prove they are the best team.
Unfortunately the "top 2 teams in the country" designation is very subjective. This year Bama and Georgia MAY be the top two teams in the country, but until they play someone from the other conferences in the playoff, they can't prove it. When they play each other, that should be enough to decide who is the better of those two teams.