The BCS eligible conference champion goes to the BCS, period. Doesn't matter how many wins or losses. It's up to the conference to determine its champion.
Now, there is the "Big East" rule, whereby if a conference's champion does not maintain at least a 12 ranking in the BCS standings over a 4 year period, then the BCS has the right to examine the conference's automatic into the BCS.
Note that it is the conference champion's ranking - not the team that won the confernce that year, but each years champions position in the BCS rankings.
The ACC does not have to wory for this year or the next - F$U was BCS ranked around #2 or #3 2 and 3 years ago. I think Maryland was around #9 last year. Obviously F$U will be ranked out of the top 10. A couple of more years like this (where the ACC champion is not ranked in the top 10 BCS), and there could be trouble. But historically, conference's rise and fall a bit.