That is a great topic to address and many (either in or departed from the faith) I think are right to ponder this question. As a believer I still have that same question too. And a question I might add to it: what makes us think that just because it seems to have come from our own thoughts or intuitions, why must this mean that it wasn’t also from the Spirit? That too, is a conjecture that I am far from sure about.
Added edit:
[one answer is … “well, my ‘thought or urge in question’ turned out to be wrong … so obviously that can’t have been from God.”
But I think even this is too simplistic, as if all our urgings are supposed to be about ‘being right about something’. If I thought I felt a nudge from the spirit to check in on somebody to make sure they were okay, and it turns out they were - no checking necessary, then I don’t think it necessarily follows that the urge (or my response to it) necessarily becomes ‘wrong’. That kind of approach is more about trying to turn the Spirit into a crystal ball to be tested, than it is about us training ourselves to live lives of faith and responsiveness. And while the ‘crystal ball’ approach to prophecy or spiritual guidance may be sexy among some, it fails to capture what most of scriptures are about, I think.]
Regarding your 2nd “more fundamental” issue … I too think there is a problem with a conception that attributes to God behavior infinitely more despicable than we ourselves (as broken sinners even!) would ever inflict on our own enemies. And saying that we sinners can’t properly recognize justice or injustice doesn’t begin to address this either as the Bible many times expects of us (even fallen as we are) to have those basic capacities in place to at least recognize justice when we see it.
I think you really ought to read George Macdonald’s written sermon “Justice” which addressed (back in the 1800s) this exact this issue you bring up. The language makes it a bit much to wade through, but I think you’ll find it an hour or two well-spent! While a lot of Christians may take offense at his approach, it is solidly scriptural, and no less a luminary than C.S. Lewis was profoundly influenced by this man.
[the link I made above often doesn’t work probably because of apparent server problems or overload on their end. Persist in trying it, and it eventually will work.]
With substantial additional edit.