This discrepancy is built into the game design and there is no getting around it - you pretty much have to do one of the two things described above.
The only way around it would be to integrate infiltrator actions to things that can happen for other reasons. You'd need some kind of crime/control system where your warehouses could get sabotaged by NPCs if they had reason. That's not a small undertaking, but until it happens, the only people who do sabotage warehouses or assassinate nobles are other nobles. That's just the way of the BM universe.
