No one else answering, so I'll have my 2 penn'orth.
I don't know the exact details of this particular exploit but yes and no.
It was probably conducted in a more remote area (IE not near Heathrow!). Airliners tend to stick to predefined corridors, so they'd pick a lauch site away from these, and a day so that the wind didn't blow the balloon into the flights.
They would have had to liaise with air traffic control and go through the notification procedures. So ATC would be aware of what they were doing and if necessary would route aircraft away.
However, the balloon was trackable (as they needed to get their camera back) so they would have known exactly where it was at all times.