For flexible envelopes this is more or less inevitable (balloon rises->atmospheric pressure drops->balloon expands->density decreases->balloon rise etc), for more rigid envelopes it is a balance that may work out in favor of the balloon staying in one piece (oscillating in altitude as it cools down/heats up again with the day/night cycle), or it may burst depending on the pressure differential. Most of them are pretty flimsy.
From: http://www.stratostar.net/faq.html
"When a balloon is filled on the ground with lift gas (helium or hydrogen), it can range in size from 2.5 ft to 8 ft in diameter. During the balloon's flight it will grow more than 4 times the diameter and upto 83 times the volume measured at launch, until it can't strech any more and will burst! A high-altitude weather balloon filled with 268 cu/ft of helium will have a diameter of about 8 ft at sea level, but as the balloon climbs through the atmosphere it will expand to 35ft in diameter and will have a volume of 22,449 cu/ft before it pops."
It will simply float to the top of the atmosphere (if it stays in one piece) to the point where the weight of the baloon is balanced by the buoyancy. Just like a rubber ball will not float 'on top' of the water that supports it but slightly inside it.
It's Archimedes' law applied to balloons.
The barrage balloons of WW-II had to be anchored very carefully to avoid having them go into the stratosphere. As the balloon expands (which it does when it goes higher) it will become more buoyant, not less so there is a positive feedback loop in there which usually ends in destruction unless you take precautions. Such anchoring requires very long cables, which makes them a bad choice to defend against jets.
So, the risks are non-zero and if one were to get sucked into a jet engine (especially the payload portion) the mayhem would be considerable, but they are so small that a 'notice to airmen' suffices unless you're operating very close to an airfield when you launch.
What is interesting about this incident is how far the balloon came down from where it was launched, it must have travelled for a long time, maybe even circumnavigated the globe more than once before landing.