Actually I'm also using lmdb (together with Python/numpy) :) Added an email address to my profile, would be happy to exchange some experiences.
But I wouldn't choose python for large scale data processing work. The python CPU/memory overhead is like 100:1, compared to C. (This is why I worked on rtorrent and ditched the original bittorrent client ASAP, and why I hate bitbake....)
The biggest problem currently is actually degrading performance, although I'm almost 100% sure that this isn't caused by lmdb itself, but rather by the bindings I've tried.
In the end, doing it directly in C is probably the only thing that will actually work.