YoI think you're right, that could be totally dangerous, if the horse isn't taught manners with CT first.
Personally I do clicker training any I don't use more than one hand. I keep my treats in a mug that's attached to my belt, but a 'fanny pack' works better if you've got one. I don't use a clicker, I make a 'smooch' noise with my mouth, to cue that he did the right thing.
I spend the first day, with 3 different 5-10 minute sessions with the horse just teaching them that mugging earns them nothing
. The way I do this is by standing beside them (or on the other side of the fence/door with a potentially aggressive or overly pushy horse) and waiting. Of course the first thing they're going to do is dive for the food. In your case I'd do this on the other side of the door/fence so as not to risk your arm (yowch!). They will try and mug, but you just ignore them, step away, just stay by their shoulder (or just out of reach out the door). The moment
they look away, even if there's a distraction, the moment they turn their head away click/smooch and treat. Feed the treat arms length away - I personally feed them just behind their chin so they need to back up a little to get it. This just helps reinforce the personal space requirement. After 2-3 sessions of this most horses are solid
that the only way to get food is by standing at a respectful distance and looking away. This also teaches them that the click/smooch means "yes, you get a treat".
From here I take it to targetting, I use a crop with colorful duct tape on the end (so they can see it easier). I hold it out, and naturally most horses will sniff it or nudge it. My mare was horrified of crops (for obvious reasons) So it took a little longer with her. I had to click/treat whenever she got close to it. Repeat until she got that, then I would touch her nose with the crop and click/treat before she fully realized and pulled away. My pony on the other hand touched the crop himself out of curiosity. You repeat this until they will touch their nose to the crop no matter where you put it, up or down or left or right, I even use it to help my mare stretch, bringing her nose all around to her sides and down between her front hooves and all.
With them both I worked on teaching them to not just touch, but to follow the crop. My pony does this to go through unmounted obstacle courses, over jumps and through tunnels and such (picture a dog agility course). My mare I used this skill to help her overcome her fear of new places/things. She was horrified of leaving her paddock, this gave her the confidence. When she was afraid of my car, I just brought her over to it using C/T following the crop, being sure to C/T just before she got too nervous to go forward again.
You can then teach them pretty much every skill with the click being the bridge to mean "yes that's what I want". You can teach them all sorts of silly tricks, but you can also teach them meaningful things, just an example: if you do dressage you can use it to motivate them to do more advanced and difficult maneuvers like Piaffes and all. You can of course carry on these skills undersaddle for when they're learning a new skill. If they won't stand still for mounting CT is a great way to help that.
Here are some videos I used to help me learn how: Video 1