In Designing a railgun to disable man-portable firearms, I asked about the specifics of the way that I had imagined for alien war-bots to disarm humans... but I was convinced by the accepted answer that my idea wasn't the best. So, I'm taking a step back and asking how.
The goal of the aliens is to prevent armed humans from damaging or destroying their war machines, and to protect the aliens and human noncombatants while allowing the aliens to go wherever they need. The means should be non-lethal and minimally- or non- harmful, and should leave the armed humans disarmed.
The means used should be as fast as possible, preferably short of causing permanent injury or death. Faster, more certain methods are preferable to slower, less certain methods. Temporary unconsciousness and/or disorientation are acceptable side-effects.
The aliens have the following technologies:
General purpose nanites/nanoassemblers that are individually as smart as a human or alien, with quantum computing capabilities and are capable of self-replication.
Nuclear batteries with an energy density 1000 times that of the highest-density chemical energy storage system. Miniaturisable fusion reactors down to 0.01m³ and 20kg.
Diametrical drives with thrust 110% of their mass, at 80% efficiency, dynamically reshapable scramjet/ramjets and Alcubierre warp drives.
Advanced IR/UV/optical and audio sensors and holographic emitters that can optically cloak an object in the visible spectrum, and auditory cloaking 99% effective up to 95dB. RF cloaking/jamming 200 years in advance of our own.
War machines (operated and maintained by nanites) with encrypted networking, perception/decision/reaction times well under 1ms, fast and accurate enough that no organic opponent can expect to prevail against them.
Weapons and explosives technology 200 years in advance of our own. Pretty much everything that we have today, just greatly refined, miniaturized and/or higher powered. Self-guided projectiles down to small-arms size. Dust-drift air current mapping. Pure fusion atomic weaponry without fission primaries.
What the aliens don't have:
Experience with human physiology or biochemistry. What they learned about humans, they got from the internet and TV shows. So, they know about human physiology, but haven't had time to fully integrate that knowledge into their weapons designs and refine them. So, no drugs or toxins (it's too easy to misjudge dosage rates) or other cutting edge (for humans) tricks. They could produce a taser or a thunderflash effect, and they have a pretty good idea of human physical/mechanical limits.
Experience with surface or subsurface waterborne combat. Capabilities equivalent to immediately post WWII.
So, what automated system could the aliens produce to non-lethally neutralize and disarm human infantry combatants as quickly and reliably as possible, from as long a range as possible, in the greatest possible numbers in the least possible time, preferably without being detected prior to, during, or after an engagement. The smaller the automatons the better, and the less the human combatants are injured the better. Human deaths should not exceed 1 in 81 if not given first aid or medical treatment.
I'm looking for an answer as quick, but better than 'shoot the weapon with a railgun on the right trajectory'.