It doesn't matter. The entire film aside from the very first fight occurs after that point. It is explained first what they are going to do and then things happen exactly how they were explained. When it happens at the end of the film, it doesn't come out of nowhere.
In The Avengers, there are two things that happen both right at the end of the movie with no build-up whatsoever and appear to happen just because the writers were in a corner and needed to get out of it. Selvig's failsafe is the first, when we were given no indication at all that Loki's mind-control could be fought off. The second is the entire alien army dropping dead for no explained reason. The former was annoying, but the latter was just ridiculous. Classic deus ex machina.
Regarding your first point: the possibility of Loki's mind-control being fought off to a very minute degree was established at the beginning of The Avengers, not by exposition but by character behavior, when Hawkeye shot Fury in the vest rather than taking the head shot. [it was discussed in deleted scenes but not in the movie itself]
As regards your second point, the hive-mind/queen-bee aspect of the Chitauri was set up subtly when Hulk took out the Leviathan and all the Chitauri yelled out in pain. While the keystone army trope is not favorite, I understand why Joss employed it as I can't think of another way off the top of my head to wrap up the story without The Avengers having to fight on for a loooong time.
Now as regards some posters feeling that there wasn't any doubt The Avengers would win, I'd argue that there were multiple points throughout the battle where it seemed like The Avengers were having a very rough go of it and for a while it even looked certain that the Chitauri would be victorious.
1. Right before Black Widow gets a boost from Captain America, she is fighting off a Chitauri soldier and she barely attains victory by the skin of her teeth and you can tell she knows they will loose if they don't figure out a way to shut off the Cube.
2. Secondly, there was a point where Cap was pinned to the ground by a Chitauri soldier and right after he defeats it, Barton informs him of the bank civilian situation and he says very wearily, "I'm on it!"
3. Right after Cap got blown through the bank window and onto the car, you could tell he had a definite "how the hell are we going to win this" moment.
4. when Hawkeye has to jump from his rooftop when he spots an entire swarm of Chitauri coming towards him and crash through the window.
5. when the Hulk was swarmed by all the Chitauri and they had him on the ropes
6. When Fury told Stark about the nuke, he had been pinned down to the ground by the Chitauri ever since he crashed through the Leviathan
7. and finally, probably the most hopeless moment was right after Cap got shot: Thor asked him if he was ready for another bout and Cap replied, "What, you gettin' sleepy?" but by the two Chris's performances in that scene that everything was pretty much going to hell in a handbasket.
Now, of course everyone know that The Avengers are going to win as the good guys most if not all action movies have to come out victorious, but the way it was executed make victory look nigh impossible.
I reposted to clearly mark Kahran Ramsus's post.