This might sound (and be) silly, but what about WiFi? WiFi works really well if it has uninterrupted line-of-sight. In South Africa I have used an Internet Connection from the roof to a repeater a few miles away half way up a mountain and from there about 30 miles or so.
Other advantages are that you'd be using cheap hardware, no transmission costs, it's easy to do data (given that's what it is made for), it's legal, etc.
The downside would be that once the balloon comes back down below a certain altitude (you can do the maths) you'd lose line of sight and all communications. But if you didn't lose it until late enough you'd have a pretty good idea where it is. And you could always revert to GSM + SMS once it was back on the ground.