I was facing a similar issue a couple of years ago, as you can see in this answer
and I ended up writing a Python script.
The post from the blog at work on three.js was also written by me and is also old.
It was written for C4D R11.5 and the API changed a bit. Vincent was kind enough to branch from my GitHub repository and update that script, which you can get from his repository.
Still the three.js script only exports geometry/meshes, but doesn't handle animation at all (morphing was not supported in three.js at the time I wrote the script (release 32))
If you want to export geometry+animation tracks(position,rotation,scale,and morphs(PLA)), you might something like an updated version of the script I had. Since it's almost two years old, it works for C4D R11.5 and Blender 2.49.
You can see a recording of how it worked here.
Still, as I mentioned above, the C4D R12 Python API changed a bit and the Blender Python API changed completely as they went for Python 3.0 from Blender 2.50 upwards.
Unfortunately, I can't commit to updating that soon due to time constraints, but I can explain/comment/share the old code if it helps.
Another thing that comes to mind is to use the older versions(C4D R11.5 and Blender 2.49), but it seems like a long way around it and maybe not all the features you use in R12 are supported in R11.5 (not sure).