Then, while you still won't be able to stop assassinations and such, just like you can't stop them now anyway, you can at least know who did it, and punish them afterwards.
That's what came up with after thinking about it for a bit. There's probably a better solution out there.
I don't want my drone to be seen at the moment of crime anyway.
Don't like drone in front of you? Accidentally throw a piece of string on it.
Even if you get criminals to comply as far as only operating drones with proper IDs, so that you can trace the legal purchase history of a drone, that doesn't mean you know who used the drone. Drones and their supporting control equipment can be stolen (and the owners prevented by force from reporting the theft) and people willing to commit assassination by drone certainly wouldn't be unwilling to commit theft, kidnapping, and/or murder of drone owners to acheive that.
Probably we're just going to have to get used to drones being around. Like we got used to cities and crowds on public streets and horseless carriages. This paranoia about drones will be seen by future historians as quaint.