There’s no great way to do this as far as I know. (someone correct me!)
Edits you make to the .js file:
69 | showHideOpacity: false,
at photo-swipe/js/photoswipe.js will be overridden whenever the plugin gets updated.
I seem to remember that you can override plugin php functions to override what JS file gets loaded, but given the size of this js file it would be less work to just go in and change that one line yourself each time you update
or contribute to the plugin so everyone can set their own options ??