All we have to do is not be certain about it. We "suspect" based on loose evidence -- that's all we have to say. She can buy it or not: we aren't lying, compromising ourselves, or saying anything falsifiable. If she decides there must be more to it -- it's not like there's evidence for her to go find. Knowledge of Homura's powers and Madoka's potential could be used to hypothesize the situation, but the time travel has to be worked out first and that requires help from Kyubey, who knows that Homura 'never' made a contract with him. Compared to the alternative of doing... What? "I don't know anything"?
If she knows about the witchbomb, and she *must*, then either she is against QB or needs to be killed, frankly.
More specifically, your assertion that saying magic made us won't help and will only tell her that there is something we aren't saying -- no. Suppose we share amnesia, waking up in alley, and knowing about puella magi system. Lack of ID, lack of connectable past. Either it's a wish -- and not ours, clearly -- or a meguca did it. Or QB, but lolno. Magic confirmed. I don't see the harm in saying that it's our working theory.
How do we explain this belief of us, in a way that won't paint a target on Madoka?
