There are a variety of obfuscation tools that make you source code hard to understand yet still have the same exact functionality. [I make one of these; see my bio].
Using any of them, you can work in the original cleartext form of your source at your development site. You can obfuscate the cleartext to produce the protected version which is then deployed. This means that people with unlimited access to the deployed server only see the obfuscated text, which makes the code very hard to understand.
Of course, you should test the obfuscated version at your development site before deploying it, to make sure the obfuscator didn't break something (or more likely, that you have misconfigured the obfuscator).
It isn't ideal; determined opponents with enough effort can probably reverse-engineer your code. Usually it is enough to discourage them and that's all you need.
Regarding encrypters: these are a very bad idea, because they include the logic to decrypt the source code. So if you deploy encrypted versions of your code, your opponent can use the decrypter you must also supply to get to the cleartext of your program pretty much trivially.
Are you afraid of “intruders” stealing your source code? Or are you afraid of “intruders” hacking your code? Either way you might be overthinking this. – JakeGould – 2015-09-19T17:30:06.650