One point of clarification -
I Google the settlement at 13b and Chase's 2012 earnings at 93b, equaling closer to 13% of annual earnings.

That being said, no, I don't think this is likely to have any direct impact on Chase's points programs. I don't have access to Chase's financials, but I'm guessing that the points programs represent a tiny fraction of the overall business. No reason to change things up due to a questionable settlement.