Fangraphs' Dave Cameron had an idea to fix the qualifying offer system, which is to turn the qualifying offer into a standing offer. That is, a player wouldn't need to reject the qualifying offer and head out into the free-agent market with draft-pick forfeiture attached and no way around it. Instead, he could test free agency, then accept the qualifying offer later if it turned out the draft-pick issue affected him too much.
The problem, as Tim pointed out, was that this idea essentially held teams hostage. It would be very bad news to low-payroll teams like the Pirates, in particular, because it would be tough for them to prepare for the following season if they had a standing $14.1 million offer out to a player that they couldn't get out of. (Example: Let's say that the Pirates had made A.J. Burnett a qualifying offer, but then given up on him and signed Ervin Santana instead. And then Burnett decided to come back and accepted the qualifying offer. For Pirates fans, that would be fantastic, but the team's accountants would probably be jumping out of windows.)
A Fangraphs reader, though, then suggested making the qualifying offer a standing offer, but making it revokable, which I assume would mean the player wasn't subject to draft-pick forfeiture anymore. This is a great idea. In Kendrys Morales' case, for example, maybe the Mariners would have revoked his qualifying offer once they acquired Corey Hart and Logan Morrison, leaving Morales as a no-strings-attached free agent.