Forgot about that part of the opening! It's been years since i saw the miniseries. I found the opening scene on youtube. Yeah, you have a point about the pipes. The camera pans slowly across them. I suppose we are to assume that the virus escaped that way.
But as the OP points out, the underground facility was sealed. It would only make sense from a safety viewpoint that it was a closed system. Nothing would be vented into the outside world.
If the virus got loose, the doors would seal and the virus would be contained. But Charles Campion took advantage of the glitch in the system and escaped. Unfortunately he was already infected.
In the miniseries when Campion gets that frantic call to close the gates, it wouldn't have made any difference anyway. A flimsy metal gate was not going to hold back an airborne virus if it escaped so easliy that it could infect Campion in a matter of minutes. If he hadn't run, all the civilians that we see on the base would've been infected within a matter of days anyway.
The only positive thing if Campion hadn't run is that the virus would've been contained ON the base. I'm sure the military was mobilizing within minutes after the outbreak happened. The Army could most likely have prevented the spread of the virus if all the victims were in one place.
But there was Campion on the run! The book says that he started passing on the disease as soon as he stopped for gas or food. And he travelled through several states before he collapsed in Texas. He likely stopped for gas and food numerous times.
But having said that, the miniseries opening is a slam bang great one even if it does strain credulity.
As for the crow/Flagg being present, I don't think he caused it. He just took advantage of it. Satan does his best work, in fact his only work, by playing on the stupidity and sinful nature of humans, in this case, pride. Those scientists and the military were so proud of themselves and mistakenly thought that they had it all under control. Yeah, when humans play God, bad stuff happens.
While watching the mini-series once more, I noticed something when Campion was running back to his house: he passed a ventilation outlet about five feet away from him. Could this have been how he got infected in the film?