If the Zend encoder is not an option, would include files to the source help?
I am just guessing, but it may be possible to include(http://your-code-source.com/?query); - or maybe a rewrite rule - that probably makes more sense. (Of course your app would have to be made ready for such calls)
Then eval the query (or url) and send information back accordingly. Your clients don't need the application code itself. If they 'must' have the application code, tell them it'll cost an extra $2400 🙂
-m.