Setting Adobe Preferences

If I'm understanding this correctly from what you're describing it sounds like your users are temporarily disabling "GPU Performance" each time they launch Illustrator. To make this a permanent change I think it's as simple as unchecking "GPU Performance" in the Illustrator prefs. You could push this out via Casper as you're suggesting but I believe it would overwrite all of the user's Illustrator prefs. If you only want to change the "GPU Performance" setting you'd have to look at doing something with a script that would edit just that setting for each user's Illustrator pref. Looks like you'd need to look for this entry:

} /Performance { /MSAAValue 0 /DisplaySetting 0 /EnableGPU_Ver19_2 1 /EnableThinFilledPaths 0 /AnimZoom 0 /EnableGPU 0 /GPUSupported 1 }

And change the "1" at the end of "/EnableGPU_Ver19_2 1" to a "0"

I wouldn't recommend FUT/FEU, as Aaron said it's smarter to target the App's preferences directly.
You can do this by dropping a script in /Applications/Adobe Illustrator CC 2015/Startup Scripts
and it will run every time the program is started.

#target illustrator

app.preferences.setBooleanPreference('Performance/EnableGPU_Ver19_2',false);

This, saved as a .jsx and installed in the path mentioned above should do the trick.

Thanks guys!
I was cagey about FUT/FEU overwriting the whole preference file and taking out the users' existing preferences, but I wasn't sure if you could script a change to the file like that. Thanks for the tips-- I'll give it a go and see if I can make it work!

For a more general description of the process, check this out as well: https://groups.google.com/forum/#!msg/macenterprise/SfbM7RD7ad4/wmu-iHau_LsJ

If you’ve ever done anything with applescript then all you have to do is look at the dictionary for the app. If you’ve never done that before. open script editor and File > Open Dictionary and point it to the Adobe app in question to see what keys/values are available.

Thanks again for the tips. I tested out @Chris script and it did exactly what I needed.
@bpavlov I'll take a look at the AppleScript option as a bit of further reading