Under the rules that were in place at the time they did NOT qualify, and it's still absolute and utter bollocks that they were allowed to do so.
By all means change the rules in future to accommodate that fact that your Cup holders might be as shite in the league as they were the following season but you CAN'T go back and change a situation that has already taken place!
They would only have done what they did for a select few teams, and most teams would have accepted it and got on with it, but of course..."this means more"
Gobshites. Hate them.