Yes. This was the position of pre-Vatican II canonists Noldin and Schmitt, that God would take care of matters on that level.
For whatever reason, God sometimes allows desecration of the Blessed Sacrament.
Even if I don't know exactly why, I think I can make some sense of it.
In a similar way as Hell, the ability to intentionally (or through gross negligence) desecrate the Blessed Sacrament seems like a logical consequence of free will. Not that God *has* to allow this, by any means. But its comparable to the Problem of Evil in a way, and just like evil is allowed (in the same sense you're talking about).
That's diifferent than allowing "desecration" for literally no purpose at all just 'cause of tiny, microscopic specks that can't be seen