How to prevent maliciously modified source code from interacting with my servers?

Title is not great but I couldn't think of a good way to word my question.

I'm trying to make some software that partially consist of other software that is under a GPL 3.0 license, meaning that, as I understand it, I will have to publish all of my source code. This is fine except that the changes I will make are (among other things) designed to limit the functionality of the GPL'd software, basically to ensure that the version of the GPL'd program interacting with the rest of the software is acting as it should be. If the users modify the source code to undo these changes, they would be able to control the GPL'd software in malicious ways.

My question is: Is there a way to ensure that the software that a user is running is the original version of my code, and not a modification of my source code, to prevent a modified version from interacting with my servers? I'm imagining some kind of checksum but I don't know much about this topic.

Thanks in advance.