There are countless incidents in movies and other media of the hero (or villain, or any other character in the thing) coming up behind unaware opponents and garroting, stabbing, choking out, or enacting other means of violence upon them.
This is my proposal for how to handle it, but I'm looking for advice and suggestions as I've waffled considerably on this.
Make an opposed Stealth vs. Vigilance check, success means you succeed in sneaking up on them, Threat means that the difficulty of your check is increased or that other special effects are cancelled out (auto crit, ignore armor, etc.)
Attack checks: Stabbing someone is Simple difficulty and, at GM discretion, ignores soak from armor (as you can slip it in between the plates in a stormtroopers armor) and automatically inflicts a Critical Injury (outright killing minions) possibly with a set result, such as Bleeding Out (if you stab someone in the neck)
Choking someone out requires an opposed Brawl check with a Boost (cancelled out by Threat, increased by Advantage) and takes rounds equal to the targets Brawn divided by 2 (rounded up). On the targets turn, they may attempt an opposed Brawl check with 1-2 Setback to escape the choke-hold. A character being choked out may not speak (all of the above would have to be modified for some species).
Knocking someone out (blunt force trauma) would simply be a Simple check as it doesn't have the same advantages as something like a knife.
Garroting someone would require an Opposed Melee vs. Brawl check and would be handled pretty much the same as choking someone out, except that it would increase the difficulty of the escape attempt once.