So no, I don't expect software created on our hardware, even developed at heart from the alien technology, to integrate with the alien hardware. It's really no different than a 19th century scientist "integrating" with Mac OSX Lion by connecting electrodes to the monitor.
However, as far as "Hollywood logic" goes, I guess it's passable.
It's not any worse than say... The plot of Hackers, DieHard 4, or any number of other movies focused around computer technology.
"Men did not love Rome because she was great. She was great because they had loved her." -- G.K. Chesterton
A fanatic is one who can't change his mind and won't change the subject.
A lie gets halfway around the world before the truth has a chance to get its pants on.