1. I have in mind putting checking procedures in certain scripts to detect any modification and then stop from working (but first the script will send me a notification).
2. I also have the idea of leaving an open door so when the scripts detects any mod and notifies me, I could shut it down via url or making the app to lock itself.
You gave me a very good idea. Instead on working with an obfuscation script I think more about encryption but not on a virtual machine basis. My first option was setting up a Linux Box and your suggestion makes me think I might have the solution on the Linux file system itself configuring the server to boot and auto login but giving no access to the files (my source code) via users and permissions. I'm researching now about the security of this approach.
I also know I can encrypt the full file system, so there goes another option. Both options offer a way to have the server running but nobody being able to access those files, it would be just as if the server was far away.