Makes sense. I suppose one way to think about it is that these are qualities which are being tested by a given situation or action, as opposed to innate skills or qualities unique to a PC. I think in the example you'd described, I'd have probably also ruled that both Guts and Guile would have to be rolled, the first as a representation of the resolve / nerve / courage it takes to directly oppose the System in a way that might harm it, and the second as a means of deciding whether the Subject in question gets found out in the process, or otherwise manages to raise any red flags. It's all abstract and interpretive, of course.
In any case, thanks for playing! I hope your session went well.