You can't write an open letter and expect patent owners to tell you if you're infringing or not. The accepted thing is to conduct patent searches (money and lawyers), and make sure that your product does not run afoul of something that's already in there.

I'm not saying that this system is ideal, (It is not! Let's make something better to replace the patent system - something based on private contract alone) but Theora is not necessarily legally OK (under the existing patent regime) just because some guy wrote a few open letters and posted them to a website.

What would I do? I would go with whatever is the better technology. (And from what I've read, Theora is a terrible format.)