I suspect that the underlying problem that the OP's GM is trying to solve is that the "Roll a d10 minus Conflict for Morality Change" doesn't take into account the number of moral choices a PC has to make in a given session. If the PCs only engage in one or two morally relevant encounters (because the PCs spent the session buying gear / crafting / planning or something else that soaked up game time) then on average they get shunted toward the light side. If the PCs do this often, then they get to the light side very quickly. So the idea behind the GM's house rule is a reasonable one --- characters who don't actively choose the light side ain't going to make LS paragon status. The implementation could use improvement.
Personally, I'd go with a "Roll a dX where X is proportional to the number of encounters where the PCs had to make a moral choice and then subtract conflict" approach to morality house rules instead.