Mercedes team chief Toto Wolff is contemplating taking disciplinary action against Hamilton.
He said it was always obvious that outgoing champion Lewis Hamilton would have to "back up" Nico Rosberg in a last ditch bid to foil the German's title bid.
Horner said he "would not have expected him to anything different".
Wolff is contemplating taking disciplinary action against Hamilton, winner of 10 races this year for the team but who lost out on the title to Rosberg by five points.
Horner said: "With where they were at, it was just down to those two guys.
"So it was only ever going to be that kind of battle between the two of them.
"Congratulations to Nico? He has driven a great season this year. He is a very worthy world champion, but it was naive to think that there would be any different approach to this race with what is at stake."
Asked how he felt the race was handled by Mercedes, he added: "We know that Toto likes to control most things in the paddock including other teams' drivers? so you could not expect any different.
"They are racing for a world championship, the drivers' world championship. There are only two guys in it and they are both in the same car?
"For Lewis, winning the race was never going to be enough for him and he drove a tactical race. He didn't do anything dirty.
"He drove a tactical race. He didn't do anything against the rules and I think it would be unfair to criticise Lewis for the way he drove.
"It was obvious that coming into the weekend that this was his only chance of achieving the result he wanted. It would be unfair to criticise him."
Hamilton's gamesmanship was questioned by his employees after he twice rejected team instructions to speed up as Rosberg came under threat from Ferrari's Sebastian Vettel.
Wolff said: "It's very simple: anarchy does not work in any team and in any company. A precedent has been set.
"Undermining a structure in public means you are putting yourself before the team."