Lots of discussion about the role of doctors in deciding for racers when they should return. It's part of the mythology of the sport, but this is the cost. Look at the tone of the story about Dr. Costa getting Doohan back on the track by stitching his legs together in Faster: it's told with a kind of awe, both for Doohan's toughness and Costa's skill.
There's no easy answer, though. Riders aren't going to make good long-term decisions, teams are often only tied to riders for a year, so may be subject to the same short-termism. Doctors can say no, but if they get too conservative, riders and teams may get litigious, saying they're denying an opportunity to win. And it's rarely life-threatening, including this situation. In this case, HRC clearly should have said no, but who knows what information they have. It's not like other team sports where the doctor works directly for the team.
I could take or leave Marquez as a person, but his talent is unquestionably among the best ever. He has an unbelievable ability to ride a bike beyond its capabilities, to go past the limits of grip and still pick up the pieces. He falls off a lot, though, and maybe he just got lucky for a long streak. I think of his opposite, Pedrosa, and his inability to fall off without breaking something and what that cost his career.
If Marquez doesn't come back, it'll be interesting for if this is a new era of parity and tight racing, or if it's just a lull until someone new takes over on the right package. HRC looked utterly lost without him, so time will tell if that's because Marquez papered over the cracks in the bike, or if it had been developed just for him to the point where nobody else could ride it...