I knew this would come up at some point! For me, he jumps at the opponent to land that header. I think it is troubling that Dermot Gallgher, having been contacted on 5 live, said it was a legal challenge; and surprisingly, I have not heard many other referees giving their view. There are so many irrelevant considerations that are murkying the waters, such as 'Alonso has his eyes firmly on the ball' or 'there's no malice', that one's only response can be to take pundits' opinions with an even greater pinch of salt than we do already. Atkinson was not ideally placed--as referees very rarely are when that kind of collision happens in that area of the pitch, especially in a phase after the ball has struck the woodwork--but his assistant perhaps should have helped him.
The more I watch it, the less convinced I am about its severity. What I believe is happening to referees at this level, unfortunately, is that they're being encouraged not to see the wood for the trees. Atkinson's uncertainty about whether the elbow contact made the challenge careless/reckless/excessively forceful may have persuaded him to call it (just about) legal to save himself the trouble of that distinction.
On a separate note, it sounds like concussion procedures were correctly implemented, for which the officials and coaching staff deserve credit after recent events.