Larian can not arbitrarily withdraw the disk version of the game. They have deals with multiple publishers (a couple of which no longer exist) and distributors, which do not involve any kind of veto on selling the game.
While I sympathize with your situation, there are lots of games that have re-releases, game of the year editions, bundles with various add-ons included, etc, and previous versions are not removed from any store inventories.
Unless you really want the support for higher resolutions, there is nothing wrong with the disk version of the game (as you noted there were only relatively minor fixes and balancing changes in the update, aside from the improved resolution support).
