From what Disney is saying now, the reason why they decided to kill off the Marvel: Avengers Alliance was because the sequel for the game was not doing as well as they thought it would. The first game was an instant hit but the sequel did not come close to achieving what the first game has achieved and because of that, Marvel decided to kill it off.
While the explanation does make sense, some people think that there is more to the story. With Marvel and Avengers being so huge now, Disney would most likely want to squeeze everything out of them. That is why some people think that Disney might have canceled off the game so that they can use the name for a new Marvel Avengers game.
Others think that Disney might be trying to move away from developing games and wants to focus more on licensing the games only.
Disney fans were not too happy with them when they canceled off the Disney Infinity game, a game that still had a large following when Disney decided to kill it off.