What I'm about to say, I say from a mercedes standpoint and not from a standpoint of favoring one driver over another. Mercedes lost two chances for a win today when they didn't make hamilton move over for rosberg. As has been pointed out, hamilton would have gotten 4th had they done that, but at the time of the call, they were looking at rosberg gaining 3-4 seconds a lap like he did at the end for the chance of a win and also the possibility of hamilton's tires holding out for the win, so when they made that call, they were looking at TWO scenarios in which a win was at least feasible. I think hamilton made the right choice for himself by not just pulling over, and I don't hold that against him. I would have said the same thing, "yo, tell rosberg to get on my gearbox and then I'll let him through, but not a moment before." The ball was dropped when mercedes didn't emphatically tell him to GET THE $#@! OVER because from their pitwall they were looking at the possibility of TWO winning scenarios, two different strategies as I mentioned above. So all in all, whatever hamilton gained by finishing ahead of rosberg, mercedes lost in the end because they don't care who wins, as long as one of them does and preferably as a one-two. Again, I'd have done the same thing as hamilton, and that's coming from an obvious rosberg fan. But I think the team may come under criticism that is reminiscent of red bull last year in malaysia when they told both drivers to turn their engines down and one was like NOPE! It's a little different cuz they got the 1-2 but I expect mercedes may take some heat over this. Or not, because so many people think hamilton shits gold 
I think the best possible finish for Rosberg was 2nd, Ricciardo was just too far ahead at that point and even with Hamilton holding Ricciardo up for a few laps i don't think Rosberg would have managed to catch him by the end of the race especially because it would have required Rosberg to overtake Alonso aswell to get any chance.
Best possible Result for Mercedes would have been to pit Hamilton instead of asking him to move over, they must have known the car would be strong at the end or they never would have asked Hamilton to move over knowing full well that it was asking Hamilton to give up on overtaking Alonso, so why not give both Mercs the chance to fight instead of telling Hamilton to give up and give Rosberg the chance? if 2nd was possible for Rosberg it was also possible for Hamilton so pitting him could have given Mercedes a 2-3 finish instead of the 3-4 they got.
They obviously had no confidence of Hamilton overtaking Alonso because asking Hamilton to move over at that point was asking Hamilton to settle for 4th place, makes no sense to me and seems like one of the worst calls Mercedes have made so far.
I don't think Rosberg is to blame, s*** happens and we only ever hear the radio messages that cause the most drama and news headlines so who knows what happened, but this was 100% down to Mercedes making an extremely bad call in my opinion which cost them atleast a 2nd podium spot.