Unfortunately that garbage happens. We never go into a situation knowing whether bonuses are involved or penalties extracted for good or bad reports. We only know that we need to be there as average customer looking for the good, the bad and the ugly. I would always answer the MSC about my findings if questioned, even though it annoys the heck out of me. A recent bad report had them questioning the equipment I used for timing and what my time points were and was I sure when it came to the 10 second rule and whether I was assisted within 4 minutes. The store put on a bad performance and they weren't going to go down without a fight. I suspect that it is the MSC having different folks handling the contact with the client that landed a series of frankly absurd questions in my email. And the most unfortunate part of this is that the some MSCs do not stand by their shoppers. I have no way of knowing how many of my shops may have been questioned in the past that were just handled by the MSC without contacting me at all.
I would tend to hold off on doing any further work for the MSC until I see how they resolve this. If you have done nothing wrong and they decide to penalize you, that would be a real indicator (to me at least) that I needed to move on. If you hear nothing more about the matter you can assume that they got it sorted out with the client and continue working with them, though you may want to avoid working the client locations that decided to fight the report. Let other shoppers visit and turn in reports that show similar cleanliness and service problems and that will make the point for you.
I would tolerate perhaps a 'give back' equivalent to that shop's fees, though I should not even be asked or forced to do that. You reported what you saw and had no reason not to be objective about it. But it would be difficult to be objective returning to that location or perhaps even working for that client in the future.
As for termination, if the company is so terrorized by the client that they terminate you over a challenged report, you need to be somewhere else anyway.