If the problem was only removing the internal classes then I would agree, but, as stated in the letter there are other issues that also need fixing.
Designing a game with modders in mind would not take more time and if done right, would save TW lots of hours refactoring an already existing codebase. Besides, I would agree with your statement if modding wasn't such a huge part of the mount and blade franchise. Not taking modding into account while designing the game is a huge missed opportunity and sadly its shows.
Fixing your code after you supposedly finished the game will take way longer than keeping the modders in mind while creating the features as you go.