I've lost all my respect for Blizzard since D3 was released, but if they do this and they improve D2 (In any way), they will definitely win me back. I don't really care if they break GoMule compatibility at all, and people shouldn't be mad or be caught off guard if Blizzard breaks compatibility with third party applications. It's the responsibility of the third party developer to maintain compatibility with upstream changes.
Any changes done to D2 would definitely improve the D2 single player experience even if most of their improvements go to the battle.net side of things. Passive improvements will affect the D2 code base as a whole, so no complaints from me on that part.
This job post is giving me hope.