You've got a pretty close minded view of the situation, it's not like Mercedes are being forced to run one car and have to pick their best horse to drive it. Hamilton's undoubtedly the better driver but if he was sacked he'd be replaced, and Mercedes might feel they'd be better off with Alonso or Ricciardo alongside Rosberg. The question isn't "if you had to pick between Hamilton and Rosberg in such a fight", it's "if you had to pick between Hamilton and someone else in such a fight". If they sacked Hamilton they'd be in the market for a world class driver, if they sacked Rosberg they'd probably be looking to replace him with a Massa, Kovalainen type driver who'll be too far behind to create any friction.
Not that I think Mercedes are thinking about replacing either driver, it's just a warning to their drivers, Hamilton moreso than Rosberg I think.