Hold them up and have them lay down. They will only then get up in response to alarm.
Or, perform a cqc combo on them. In ground zeroes, this keeps them knocked out indefinitely until awakened by others.
No but I mean like really get rid of them all together like throwing them off a cliff does. That doesn't count as a kill for whatever reason.
Also you're right about the hold up keeping them down until a base alert or someone comes to get them, but the CQC combo is 4 minutes iirc.