There's one potential for danger, which is DNS tunneling. Devicescape and other authentication systems work at hotspots by sending particular DNS queries through to remote servers that respond with information in special text records that can provide login credentials and other information. DNS is proxied and often scrubbed for hotspots, however, and I suspect that Aircell figured this out in advance.
On the cell side, only a handful of planes in Europe and the Middle East are flying with picocells on board that can be used to establish a phone connection via a satellite data link. A number of elements would also need to be in place for a remote connection to be established. A timer or air-to-ground cell link would be much more reliable.
I expect that authorities will scrutinize in-flight cell and Wi-Fi service for additional weaknesses, but I doubt any ban will be put in place.
Southwest Sets In-Flight Wi-Fi at $5