module_name.php
file can't be overridden.
Check to see if the module has options to disable the loading of its scripts - Many modules come with such settings.
If it hasn't, then you could propose this to the developers of the modules to include it in the next release.
You can always clone the module and make one of yours that will behave the way you want.
You can simply "hack" the part of the code of the module to make it work the way you want ... just remember to come back to it if you ever update it to re-do your
hack.
Depending on the scripts and the way they are injected to your page by the module there are techniques where you can manage what scripts you want to keep or disable. There are for example plugins like jQuery Easy or JCC - JS CSS Control and others that allow control over which scripts are getting on the page.
Also check this Q/A for how to remove files from the head via code:
Disable script loading in head