I don't know if this will help, but basically I think this is the way that Apple sees it.
Apple will take your old machine, and replace anything/everything in order to be able to make it a refurb. Apple feels it is their obligation to replace anything that was not right as per Apple's responsibility.
Since you broke the trackpad, that is not something that Apple is responsible for. Had you not broken that trackpad, and everything else still went south, and they did the trade-in for you, they would not have to put a new trackpad into the machine to bring it back to refurb status. Since they have to replace the trackpad, and it wasn't their manufacturing that was at fault, it should be you who pays for that part, even though you are getting a new machine. Even with any other issues that trackpad was perfectly fine before your coffee mug landed on it. Heck it even still works afterwords, but obviously is not in a condition where it would be considered acceptable to be sold as a refurb.
Personally I think Apple is doing you right. And initially I think you realized it. Probably many people will disagree with this. But the reality is that the trackpad would not have required replacement if it was not for the accidental damage you are responsible for.