I don't think Atkinson can be blamed too much for not allowing play to continue further because there was a big tussle between Altidore and Sagna with the end result being the Altidore was pushed wide away from goal. So in the referee's view he had arguably let the play run a bit before blowing the whistle anyway. The goal definitely shouldn't have stood because he'd already blown his whistle before it went in.
Only point of debate for me is whether it should have been a red card, I think if he gives a freekick then it probably should be a red; possibly he wasn't 100% sure in his mind what went on because Altidore was groping Sagna as well and maybe there was a sliver of doubt in terms of whether he thought that was simply trying to free himself from Sagna or more of a 'six and two threes' type affair so he didn't want to dismiss a player if he could have a case to answer in that regard.
The thing is after seeing a replay later on, he blows right AFTER Altidore actually gets away from Sagna and that is what makes it a horrendous decision by the ref. Sometimes ref's blow too early and then the player gets away from a foul , but the ref didn't know he would get away. But here he blew the whistle just after Altidore shrugged him off and started towards the ball, there was no reason to blow the whistle then, either as he's being held(too early still but less bad) or once the player has gone beyond the foul you have to give at that point 3-4 seconds to see if an advantage develops. You can't blow after the player gets away but before the advantage, its 100% wrong to do it at that point.
I really can't see how it's not a red after the whistle is blown though, same as Luiz, he yanked someone down on the half way line, but it was what Mirallas and Mikel wasn't particularly close(only because of the holding did he get close to level but he was still 5-10 yards over and he's a much slower player than Mirallas. Without the holding Mirallas would have been clean away and Mikel zero chance of catching him.
The thing is, when you look at the replay for Sagna... what the hell was he doing, I just don't know, where is putting both arms around a player and not even looking at the ball a good idea. This wasn't a mistimed tackle or a sliding tackle where he may have gotten the ball, it was so blatant, so utterly stupid. This is why he isn't good CB cover, or a good fullback, he does utterly stupid things so consistently.... so does Kos. There is a reason why we still had at least 2/3rds of the way into last season the highest number of individual errors... a HUGE amount of luck last year meant we didn't concede but we were making the errors all season, awful errors.
Kos would make less errors with better defenders around him, but better defenders around him he certainly needs. Verm got a huge amount of unfair criticism in the last two years, a HUGE portion of his "mistakes" were because he was out of position covering for our other defenders huge blunders. It was his pace, quality and reading of the game that let him get in position to attempt to correct the others mistakes... blaming him for not being able to fix them all is so stupid. Really hope he can have a good uninjured year as I still think him and Kos can be a great partnership.