That's interesting, because any time you see pictures of people watching 3D movies from back in the day (usually in period films made after the fact), the audiences are wearing anaglyph glasses, the "famous" ones with the white cardboard frames.
If those weren't used, then where did they come from? Maybe home presentation? Broadcast, then later VHS and DVD, using anaglyph? Did black & white films use polarization as well? I'm not disputing the idea, I'm just curious.
I'm thinking more of the projection side than the capture.. I'm sure the capture was always done the way it is now. For an old movie shot in 3D, it would simply be a matter of going back to the negatives, or some original print that still had the different views separated out as full color images. Using today's technology, putting that together would be a snap. I imagine the OP is referring to using an anaglyph source as trying to extract two full-color frames from that. I'm not even sure that's possible. It's easy with black & white, I've done it myself, but I've never had any luck with color photos.
Welcome to Rivendell, Mister Anderson.