I think it should be an option, definitely. Especially since it’s just one scene, you wouldn’t even notice that the shift had happened, especially if they used the digital IMAX crop.
Before I broke the external Blu-ray player for my MacBook, I was able to use the software I’d purchased to watch 3D Blu-rays. I confirmed with the 3D Guardians of the Galaxy that you should be able to just grab one of the eyes and have a 2D IMAX ratio capture.