I love it how "some" people hated the magical(ish) background and said "No! dis is sci-fi game! no magic derp" and there you have it: Magic scrolls, flaming swords, swords that shoot bubbles, maces that has bones flying off when you smash with them, you cant argue that this is a sci-fi game if it already has magic in it. So i would like to kindly say one thing to those people: In. Your. Face.
Sciency magic could work. I mean we already have a glitch wizard but all he sells is stimpacks and a wizard hat. Some might call it a health potion, though its just a stimpack. Aslong as any magic weapon or tool is implemented by the means of science then im sure things that are sortof like magic will be fine.
The Glitch are likely to refer to some technology as magic, yes, although that has more to do with their culture than anything else.