Quite frankly, there aren’t that many truly-spectacular ideas or methods to be found in either the source-code or the executable-code of any computer program.   (Despite the proliferation of “software patents.”)   Of far more concern to you should be the potential instability and un-maintainability that such attempts at “protection” may introduce for your paying customers.   This is the outcome that Mister Market will never accept.

If the source-code is proprietary, first license it (engaging the services of an Intellectual Property attorney who knows his stuff).   But thereafter, focus on what the customer needs in order to use your source-code and be delighted with the total experience.   Encryption, and even “minifying,” only gets in the way, while bringing nothing of value to the table.   (And if you have ever been on a diagnostic team that is trying to troubleshoot an issue raised by a customer who is paying for support, given only error-messages produced by minified code, you will know precisely what I am talking about ...)