You can't keep the functionality of your software a secret and still distribute it.
What goes back to the initial reply you got, nobody every read a software patent to understand an algorithm. People would rather decompile and deobfuscate your binary. What has the added benefit that your binary actually contains the algorithm, while most software patents do not really disclose the thing they are reserving.
Algorithm secrecy was historically never a problem in software. Currently with the cloud and SaaS it is starting to be a very narrow one here or there, but since software started being protected, patents never disclosed the things they protected, and there's no movement on making they start to do that.