I suspect, probably not too much of stretch, that Jack isn't exposed to the BIOLOGICAL WEAPON. Either he was just exposed to the device's refrigerant, the bio weapon isn't a virulent as we may suspect, or it was a benign decoy device. Obviously there's no way Jack was exposed to something severe and will die. At "worst" it'll slow him down over the rest of the "day" and he'll be cured between seasons. Anyone remember his severe heart trouble at the end of Season 2?
And, yeah, Harvey is definitely coming around to the Ways of Jack.
Well, there is such a thing as the human immune system, which is one of the many reasons why bioweapons are a crapshoot. It's also possible that Starkwood designed their weapon to be used on the battlefield, rather than as a weapon of terror, in which case they would have gone with something that is incapacitating but not deadly. The big idea behind using bioweapons isn't to kill huge numbers so much as it is to make the enemy so sick that none of them can fight back. Assuming that they originally wanted it to pacify urban areas to make it easier to get to insurgents, a less-lethal bioweapon makes sense. Puking civilians can be a mild PR hit. Dead civilians, substantially worse.