So they don't want Palmer flying the helicopter. But MacCready who has been drinking is a good choice.

This was in the early 80s. Drinking made you drive/fly better back then.

He was pretty much drinking every day from what I could tell, however it is clear that he was quite a good helicopter pilot even with it in his system. He demonstrated sensible / procedural takeoffs and landings, although that was just the film pilot that we saw on screen of course. So they would have been used to his behaviour and flying abilities.

Palmer was stoned all the time

It's a funny moment, but weed had a much more negative connotation in the 80's than it does now, I mean back then people compared it to heroin or meth. I also think MacReady just commanded more respect than Palmer or anyone else at Outpost 31, which is why he so seamlessly assumes power.