[Patashu]

Here's what I'd do to transition to non-combo-based scoring:
Update the engine so it sends both your combo based and non combo based score.
The site keeps track of your best score of both, but everyone can only see the combo based one.
When enough people have played such that the non combo based high score tables will be filled up, transition the entire site to the non combo based scores by pruning every score that has a miss in it.