I know that everyone ("everyone") hates software patents.
Personally, I don't see what the difference is between patenting something made out of atoms that accomplishes a task in a new way, and patenting something made out of bits or memes that accomplishes a task in a new way.
If (a) you've come up with something new; (b) you're not morally opposed to software patents; (c) you have ~ $5k ; (d) you'll be able to detect infringers ; (e) the infringers will have deep pockets, then a software patent might be the right tool for the job. You can slap "patent pending" on long before the patent is issued, and collect licensing fees from legitimate companies that want to use your technology.
...all of which gets us back to the core point:
What is it that you hope to accomplish by obfuscating / patenting / whatever ?
A moral victory?
A competitive advantage for a few months?
Other?
Your answer to this question will dictate how you proceed.