I understand why reputation decay is present - I've used similar techniques myself.
However it should be a smaller, slower component that it is at present - especially as the game runs in realtime. Very annoying if you only get to play once or twice a week (or fortnight).
This could be balanced by more negative rep effects for Allied players on missions which benefit factions with whom the Major Power is in conflict. This reflects that being Allied comes with greater responsibility to uphold the ethics/politics of the Major Power than would be the case for just Friendly.