You think that rule is not right, but playing with a A and a B team in the same division isn't right either
IMO. Even the so-called satellite clubs shouldn't be able to compete in the same competition according to me.
In Belgium for example, there is a team called GBA (Germinal Beerschot Antwerpen) which was owned by Ajax. If GBA would have performed well in the league and say got into Uefa-cup in the same season as Ajax, then GBA wouldn't have been allowed to play European Football. That, I think is a very good rule, as discussions would be endless if they'd play against eachother.
And say they'd just decide no team gets promoted nor relegated, it wouldn't be fair either. I think there is no good rule for those situations.