As far as I understand it, proxying it is dangerous because IPFS will announce all your IPs so that the shortest routes can be established. You probably need to run it in a VM/container that only has access to Tor and no other network adapter.
Thanks! We're hard at work making everything better, especially the documentation and examples bit, but lots of work on the APIs as well.
If you have anything concrete to suggest or help out with, please open up a issue in the relevant repository, this would be the entrypoint to find your way around in our Github organization: https://github.com/ipfs/ipfs