I was thinking of doing something like this myself, I'd have replied sooner only I couldn't find a link I wanted to share.
I think google only looks (afaik) at the site content not the actual coded html/php part, (but don't quote me, it's only a guess) so for proxies it could be worth encrypting the main.php template page and then having the contents (config.php) in plain text so the bots can still read it for the ads. I was seriously considering encoding the templates on my proxy themes site so they couldn't be altered but I've resisted so far. I've found a few of the users removing backlinks, against the terms, and adding their own, disrespectful to say the least. Encoding the main.php was one of the things I was going to do for new themes, that would stop any alterations, and still allow plain text contents. It's not been a priority though so it's still on my 'to do' list. I'll more likely do all the templates when I (eventually) revamp the whole site so maybe some testing is called for.
The backlinks would also want to be un-encoded to be seen easily by the listing scripts, the glype footer link might be different but that can be removed anyway if you know how, I don't think that's so important imho, as long as it can be seen in the displayed page. I'm also not sure how the other links, like the terms/privacy/cookies etc. would react if encoded, they might have to be left plain to work (the <!-- CONTENT START/END --> tags).
The one thing I'm not so sure about though is if there's any speed penalties or extra cpu cycles needed for rendering the pages, it could have a negative effect on server/vps performance or user loading times. Sometimes I wish I knew more about these things so I could test properly.
My two penneth (and cheap at the price).