I'm not so sure now I've read a couple of forum questions on this - but I always thought that part of the lockdown procedure at the Project Blue facility was to flood it with fast-acting nerve toxin. Everyone in there would be dead anyway, and it would prevent transmission (except for that one pesky gate guard). But this appears not be supported by the book or mini-series.
As far as can be gathered from the book, and from looking at other diseases, the rapid action of the virus in the facility is possibly down to two factors:
a) amount of exposure - the leading theory on surviving Ebola pretty much boils down to how much virus you get infected with - it simply overwhelms the immune system if you're infected with a sufficient amount, but under a certain threshold and you may be able to fight it off. Since the air in the lab was likely saturated with the virus, it quickly overwhelmed the immune systems of the staff in the lab - causing them to collapse and then die very quickly.
b) the virus was designed to kill fast, and then mutated into a slower acting virus. Viruses have extremely high mutation rates per generation (compared to other lifeforms), and also have very short time between generations. By the time the virus is out in the world, we see some extreme variability in time between infection and death.
One last observation - we don't really know how much time occurred between infection and death for the people in Project Blue (although, I agree, it does look it was pretty sudden). The soup guy might have been symptomatic for hours or even a couple of days - he could have just been eating some soup in that short period where people seemed to rally (we see quite a few people in the book have their symptoms temporarily improve before death), and then he collapsed and died.