I thought the only time an airline would take issue with sedating a pet was if the animal was oversedated (just the other night, on the show "Airport," one of the animal handlers at Heathrow mentioned a cat appearing oversedated, but didn't say anything about sedation itself being against policy). I think it must be a matter of a particular airline's rules, particularly if a vet can confirm that the animal is at a safe medication level. I can understand the drop-in-blood-pressure concern, but sedated animals being more at risk for broken bones seems counterintuitive. Just as doctors say, for instance, that someone who's had a few drinks and fallen down a flight of stairs or something would fare better because his or her body was more relaxed (that is, not tensed up in reaction to falling), I'd think it would be the same for animals in turbulence. But who knows--any vets out there?
Also, I don't know what the rules of carrying animals onboard are anymore, but six or so years ago, one of my brothers had a German girlfriend who used to fly back and forth with her rat terrier (what a name--they're very similar to Jack Russell terriers, but slightly smaller) on board with her. Of course, all the rules could have changed by now. Anyway, if you haven't done so already, check out all the airlines, instead of the one (or ones) you've been used to flying with. You never know...