I'm watching "Hot Zone", and I've noticed that if John had obeyed Elizabeth and stayed in the gym, Atlantis would have been much worse off.
Peterson was heading for the control room with no signs of stopping. John disobeyed Elizabeth and went after him, which caused Peterson - by accident - to come out into the mess hall. Atlantis recognized the threat and locked down, including locking everyone in the control room out of the mainframe. If John had stayed in the gym, Peterson would have reached the control room - or at least gotten close to it, infecting who knows how many - and Atlantis would have went into lockdown, locking the control room out of the mainframe anyway. This would have locked John and Teyla in, as well.
This means that only Carson and his team would be able to move about (since Atlantis recognized that people in hazmat suits were safe and allowed them to wander). It would have taken some time to send a gene carrier in a hazmat suit to get the bomb and then head for the Jumper Bay. In the meantime, I'm willing to bet a good number of Rodney's people would have died - including Zelenka and Ford, as well as any people in the area Peterson would have been in before Atlantis locked down.
Plus? They may have lost the jumper and the pilot, since all of Carson's people are in the medical field - most likely not someone who has had anything approaching the training to fly up, drop a bomb, and make like a bat out of hell.
So the dead would have been:
Ford, Zelenka, and most likley more scientists in the outskirts of Atlantis.
Peterson and anyone he encountered, including the possibility of those in the control room (depending on how far into the main part of the city he gets).
The pilot (and one jumper)
John disobeyed orders, but really - thank god he did.