Thanks for the responses, I was afraid I might be lambasted for letting my dog bark at someone- I have already beaten myself up over that again and again.
I think it is worth training for 100% (or as close as possible) control over my malinois. She is a strong dog with a bit of reactivity which is normal for the breed but not something to take lightly. People also carry guns when hiking, for bear protection. There is no reason I should risk this happening again and not being so lucky. If we turn a corner on a trail and encounter someone acting strangely unexpectedly, I still want to have a 100% recall on my dog. She may have been reacting to the guy being sketchy, but doing so made me less safe, not more. I need to be able to control her in this type of situation.
Skijoring is really fun- I will post a recent video. We haven't had much snow in town yet, which is why we travelled to the remote area to skijor. I don't think I'll be going there again anytime soon.
The guy pulled the gun out of his chest holster but didn't point it at me. This was during the conversation post-encounter. That was enough to shake me up pretty good.
I think half of the problem was that we startled him. He was walking along on a remote trail and was suddenly being barked at. Had I called out, etc. he may not have had quite as severe a reaction. I have been yelled at when skijoring for passing someone too fast- even though I have bells on the dogs' harnesses and also yell out when I see someone to let them know I am coming by. And this is when the dogs do nothing wrong and just pull silently in harness. So, trail-user conflict was probably part of it. Those can get ugly even without a barking dog being involved.
Also, my malinois looks scary when barking- her teeth are very white, she has a black face and muzzle, she has pointy ears. She looks like a typical vision of a vicious police dog. She never charged the guy or remotely tried to bite him, but she was trying to look scary, I'm sure, and apparently succeeded.
I'm still feeling shaken up, but it is always good to have motivation to get out and train, especially at 0 degrees F.