You're going to have both the organization and the fighter's talking out of their ***** regarding this decision. Hendo is upset (or at the very least cynical via his twitter), yet Dana and the UFC named Lyoto the number one challenger after defeating Bader (in August) and Lyoto declined to fight Jones on short notice after the Henderson injury. I don't think there was any single decision that made perfect matchmaking or business sense.
Henderson isn't really getting a raw deal at all other than facing the 'twilight' of his career with the uncertainty of whether he gets another title shot [payday] in the future. It sucks, especially for a legend of the sport, but that's the fight game in a nutshell.
The sentiment that this somehow damages the integrity of the MMA as a sport is a ludicrous non-starter.