This accusation demonstrates the accuser's own lack of understanding about computers; Hollywood actually got this one right. Personally, I rather suspect this was coincidence rather than anybody on the production sitting down and working out this logic. But nevertheless, the movie is right on this point.
There are similar scenes in other media that are ludicrous. I am pretty sure I recall a scene in Voyager in a later season where the crew encounters a computer they've never seen before, from a species they'd never encountered before, on a piece of hardware they have only a vague idea what it does. They beam aboard, stand in front of a console, discover they're locked out, and "hack" past that in about literally 5 seconds. This is stupid. They shouldn't even be able to read the text on the console, and they've "hacked" it in five seconds. One wonders what the hack exactly was. Hollywood makes this mistake enough that I'm pretty sure that Independence Day getting it right was just a coincidence. Probably if the story didn't include a downed fighter being studied for decades they would still have rolled with the virus idea. Then it would have been silly. But as written, it is not silly.