I still hold firmly to anything you change after origin, affects the origin stats (ie. the income in this case)
If I recall though, during the exact order of character creation, a player selects Origin before Career (DH CRB p.13). Noble/Famulous Protege are Homeworld origins, and define the monthly income at that exact point. From there, any career chosen next is going to have a "lower" monthly income. So either there is a caveat in the income replacement from the homeworld, you naturally go with the highest, or you go with the most appropriate.
It sounds to me like the player in question is choosing Banisher for ability/some fluff reasons, but is trying to make use of their wealth.
I can't remember if this is the case or not, but is Banisher limited to rank 1 clerics only? That is to say, is it only available as a rank replacement to characters being created? If so I would say they can keep their noble grade wealth. If it can be selected at any level, that indicates that Banisher is meant to bring a cleric down from their paygrade.