This all boils down to Hamilton's second pit stop. They should have put him on the option tyre with the intention of doing 2 15 lap stints.
The last 4 laps he did on 30 lap old options when in clear air averaged out to 1:27.750, he obviously had a lot of pace even on worn option tyres and the prime were not showing any longevity benefits over the option for the entire weekend, why Merc though the prime was a better choice than the option baffles me.
When Nico got into clear air after his pit stop and before he got behind Lewis his lap times were about 2s faster than prior to his stop, granted he was being held up a bit by Kyvat a bit but as he was not able to overtake the performance deficit was less than 1s/lap so lets assume that Hamilton would have been 1s/lap faster on his new options than on his worn options (I think this is a conservative estimate but still) This would have put him in the 26.75's this would have been 1.5s/lap faster than his mediums between laps 40 and 55.
Over the 15 lap stint that would have meant he was 22.5s faster than he was on the prime, he would have caught and overtaken both Alonso and Massa. Ricciardo was doing 1:28.5's during that period so it is also possible he could have over taken him as well and had a slight lead going into the pit stop phase on lap 55. At the very leas he would have been right on Ricciardo's gear box going into the pit stops and then it would have been a 15 lap battle for 1st.
This would have also meant that Nico was not held up by Hamilton for 11 laps which would have gained him ~ 10s provided he could overtake Alonso swiftly.
This strategy would have guaranteed Merc atleast a 2-3 and a 1-2 was possible if Lewis and Nico had got the overtaking done.
All this talk of Lewis holding up Nico is besides the point, if the team had chosen the right strategy both cars would have done better than they did and the team orders fiasco would never have come about and we would all be talking about a stunning race without the controversy. Ultimately it was the strategy that Merc chose for Lewis that cost them points, not what the drivers did on track.