Something about the tone of the initial post, and those threads running up to the wedding, tells me this has been a very laboured event for you and the current dilemma is the bad icing on the cake of the stream of events. With that in mind, I'm inclined to see that you're seeking some sort of what I call "emotional compensation" and by not stretching even further you'd feel better about having some control of some things. In any case, I'd say make a contribution and get it over and done with. If you don't, it may linger in your head much longer than you want (the fact you have a dilemma in the first lace suggests that) - if you do, it's the final financial stretch and you'll know you no longer owe nothing to anyone.
The thread is a fascinating read and brings up just how complicated weddings and etiquette is; add to that all sorts of cultural issues and I begin to wonder all sorts of things. And FWIW, I do not consider contribution to the honeymoon odd at all. I've come across them in weddings from NA and European acquaintances, and being practical I actually like that there are no grey areas but straightforwardness. If everyone is aware there will be spending on the tokens that mark the occasion, why wouldn't it be for something the couple really wants? Hence the registries. Would you raise an eyebrow if they wanted contributions for some charitable cause? The only thing I'd have an issue is the type of the honeymoon the couple wants and whether it's way above their lifestyle - in such case, expecting the guests to know they should reach deeper in the pockets is plain arrogant. But, even in such case, they should have worried before about what would happen IF they don't raise enough to cover the trip.
Either way, I'd close this chapter in the simplest possible way (whatever you feel now will wear off in one year time, I can guarantee you that) and remember the fact you had the opportunity to dress up. I saw that selfie, you looked amazing!