Actually he's raising his arm to block its head from the flames. He also does the same animation as soon as you raise the flamer at him, without pulling the trigger. In stead of charging, he will shield away a little, then slowly stalk towards you. You need to watch the range and hit him with a full second of flames instead of just tapping the trigger to chase him away.
Other things you can try is to cycle through your items, even the ones that don't seem to do much can still cause a distraction. I've used a flashbang and smoke grenade to great effectiveness at times, distracting it with the flash followed by smoking out the place before creeping down the corridor. Helped alot in medical.
And also, using the wrench to bang against the wall is a great way to trick the Alien into going after a flare or cause a distraction. A couple of times I would bang against one side of a wall, walk across to the other end of the room, watch the alien run right pass me, and examine the wall I banged, while I walked out the door it just came in through.
Don't use the noisemaker and flares too much, those are the items it gets used to the quickest.