While I perfectly understand you about not wanting to make changes that would lead to massive user complaints, can we possibly have this feature as on opt-in one, which comes with some nice big warnings about the possible side effects?
This way the average user would be happy without any glitches, and the advanced users would have a chance to balance between having transparency or clean 3D view.
Not to mention the chance that a possible real solution is found if the transparency feature is used by more and more people.
So please-please reconsider!