Don't forget, one of the beauties of CG animation is that it is mostly constructed using 3D objects based in 3D environments (some elements may still be 2D, like backgrounds for example) and then flattened down to 2D for the 2D release. So as long as you still have all the original data files, which I'd be very surprised if a company as big as Pixar didn't, you can go back and reload the original files and then re-render the film but as a stereo output or using two seperate offset 'camera' views. However, it will still require the skills of the best stereographers to make sure that the shots still work together correctly. However, it is not the same as making faux 3D live action movies from their 2D counterparts, which can, as many folk have discovered, be a rather more miss than hit result !
Really interesting article here if you fancy a read....
http://www.fxguide.com/featured/art-of-stereo-conversion-2d-to-3d-2012/