That's such a damn shame. Why would they ever want to become an affiliate with a modding organisation and then stop them modding?
You'll find that a lot of times there is a disconnect between what the company wants and what the lawyers want. The lawyers were probably covering all their bases, and the company wasn't aware of the ramifications. And, as often happens in legalese, the agreement didn't specifically that we had to stop modding, it was merely the natural interpretation of the wording. (E.g. "you may not produce any derivative works of the product".)
As for why they never got back to us, I can think of three reasons: a) it got lost in the to-do list, b) the lawyers convinced the company it was too risky to change the agreement, c) the GOG executives truly do not want to allow mods. I think c) is unlikely.