Stopping the destruction of cities isn't the point. That's putting one side to a standard that is a no win scenario, which somewhat obviates the entire point of the vs scenario. You might as well go with, "Well, what if the ID4 faction pops into the inside of the Avengers HQ in the blink of an eye and fires at them point blank before they can even react, and Stark has no Armor, and it's the Thor who got stripped of his powers, and Banner hasn't tried his experiment yet, and Romanov is still a little girl pre- training, and Cap is still the wimpy kid from Brooklyn, and..."
The point isn't whether or not they save everyone, or even anyone. It's whether they come out on top in the end.
And yes,
in the end, they would. They might not save New York. Or any other major city. Stark's base isn't
in New York, or even L.A.
His base is somewhere outside Malibu. And he's the only one who needs a "home base" -- Cap's skills are all integral to his physiology, as are Banner's, as are Romanov's, as are Barton's. Thor's skills are
maybe external to his physiology, but unless you're proposing the ID4 faction takes on Asgaard, which is outside the OP, they can't touch the source of his abilities.
Going to observed tactics, we've seen that the ID4 faction uses scouts. If they can employ FTL propulsion, the MCU Earth -- being too thorny to tackle -- would logically be passed by. If they
don't, the MCU Earth is
still too thorny to tackle, but assuming they have no choice but to try for it anyway, they are definitely so limited, propulsion-wise, that the MCU Earth was their best shot at survival -- as determined by scouts. There is absolutely
nothing in the MCU Earth scenario that changes whether or not that scout crashed.
Since it did in the ID4 ficton, and since nothing in the 1940s (or, being generous, the 1950s) MCU Earth was radically different,
weather-wise, there's no reason to insert an unknown variable that allows their scout to escape that same fate.
Parsimony. No introduction of superfluous variables. Unless you can explain,
concretely, why the ID4 scout did
not crash in this scenario, there is no solid foundation for the assumption that anything different happened. Logically, for the mothership to make the trip, there had to be a reason. The most logical reason was a favorable report from a scoutship. The ID4 ficton established that said scoutship crashed on Earth and was recovered and subsequently studied by humans. Unless you can show a canonical difference in the MCU that would actively
prevent the crash and/or capture of that scoutship, that scoutship crashed and was captured. Necessarily,
per the OP scenario. The ID4 mothership
would not arrive without that event. It is the cause, of which the arrival of the mothership is the effect.
And then we get into this thorny little question:
Which Tony Stark is the MCU Stark? Because the closest match is the
Earth 616 Stark, who is the
owner of Area 51. So yes, he'd know about the crashed alien scoutship. And knowing his character, he'd know about it
intimately by the time of the events of The Avengers.
Additionally, having the ID4 faction sling comets at Earth in order to dispose of the Avengers before the aliens arrive is cheating -- they don't know,
until they arrive, that they're going to have to contend with that threat. So, no, they're
not throwing rocks at the planet they've just burnt who-even-knows-how-much fuel to reach in hopes of finding a planet to perch on until they use it up and head for the next one.
So, no. There's no cutting out the ID4 faction's weaknesses. There's no "total victory" for the Avengers, but we're not holding them to that standard, anyway, we're holding them to this one:
Could they do what a ravaged and threadbare mundane team of humans did in the same position. Yes. Without the faintest trace of a doubt, they could.
Without FTL, the ID4 aliens would take enough time to arrive that the Avengers could have a plan ready and waiting so that they could thrash the Chitauri and Loki as was done on screen, and still bitchslap the ID4 aliens as an
afterthought.
