@holt
Not really. If you did that, it would be unfair to the teams that are in the "worse" leagues, which isnt fair to anyone. I think it should be based on the opposition, for example I have ~3.5m, so if I win against someone with 5m popularity I should be more rewarded by winning than if I win against someone with 1m popularity.
In the end, maybe you could be benefited in the league ranking. For example, in Portugal you would expect Ala-Arriba to win, Sporting and União to fight for second position (the difference in popularity is not significant), and if they finished in lower positions maybe get a small popularity hit with some fanclubs being turned to casual or normal fans (which means that they still can get them back if they start winning again so that the hit isnt that significant).
On the opposite side, if MJJ with just 1.4m fans manages to not be relegated, he should get a big increase in popularity since he has 2/3 of the next team's popularity and by staying in the league he did the "impossible" and proved to be a good manager, therefore he should be rewarded.