Unfortunately, there is no accommodation to make movies 3D for someone with only one functioning eye.
He SHOULD have been able to see the movie clearly with his one eye, using the 3D glasses. Using 2 pairs of 3D glasses would not help and might make it less clear because of how the lenses work.
Here is something I first posted a few years ago about 3D movies with only one working eye.
Here are my thoughts about the 3D shows:
Mickey's Philharmagic at MK - the music is very good and the show would still be enjoyable even if you could not see the pictures. The pictures are also really good and would be worth seeing even without the music. This is the newest movie and has the best pictures and best 3D effects. It includes scenes from Aladdin, Little Mermaid, Beauty and the Beast, Peter Pan, Lion King among others. The story line is very simple - Donald Duck put on Mickey's magic hat, which flew off his head and keeps flying away from him. He spends the movie chasing the hat through scenes from different movies.
Bug's Life at AK - I would skip this one with small children. The audience is shrunk to the size of bugs and gets an introduction to bugs. I have never been in this show without someone carrying a screaming preschooler out. Some of the scary things include a friendly bug that 'sprays' the audience with stink bug scent, a friendly bug that 'sprays' the audience with 'acid', Hopper (the 'evil bug' of the movie) bigger than most kid's dads, and angry bugs 'spraying' the audience with bug spray, swatting with fly swatters, spiders falling from the ceiling and wasps coming to 'sting' the audience. It is newer than the Muppets movie and does have some good effects, even without two eye vision.
Muppets 3D at the Studio - There is more 'talk' in this movie as the Muppet characters explain what they are doing/what's happening. Some of those sections do not really look terribly 3D, even for someone with 2 eyed vision. The movie is cute and does have some musical numbers.
About the 3D effects; as was already described, the technology in the movies use polarized lenses. So, viewed thru one eye, there will still be a clear image. I have personally tested it out by closing one eye in the 3D movies and the movie is still pretty clear - Mickeys Philharmagic being the best (probably because it is the newest).
On one visit a few years ago, my oldest DD and her DH were with us. My son in law has MS and was recovering from an MS episode when we went to WDW. One of the effects of his episode was that he had lost most vision in one eye (don't worry, it's all back now). The reason I mention it is that he is someone who previously had 3D vision and temporarily did not. He saw all the movies (except
Honey I Shrunk the Audience - which is no longer playing) and said none of them gave him a headache. He had a patch over his bad eye, so was not using it at all.
He said that Mickey's Philharmagic was really well done and did give a 3D appearance, even when viewed with one eye.
He is an artist (specifically, a comic book artist - and specifically in comics, his specialty is inking. The inker emphasizes lines and puts in shadows, highlights (and uses color, in color comics) to give an illusion of some things being farther back and some closer. He explained that they use the same techniques in the 3D movies to make things look 3D. You can even see that in 2D movies like the picture from Buzz Lightyear, which also uses depth of field (the less clear items in the background):
The polarized lenses intensify the effect, but the colors, shadows and art put into making the film in the first place are what gives the 3D 'look' in the first place.
The newest 3D movie is Mickeys Philharmagic, so it uses the best technology.
The oldest movie currently showing is Captain EO, which has parts that dont look 3D, even for people with good vision in both eyes.