Miller does come out of those trailers looking pretty sinister, but it's hard to say.
Signs that Miller could become Big Boss's enemy:
1. In the trailers, he appears to be overseeing the torture of what looks like Huey and Quiet, who are presumably good guys.
2. He ends up apparently opposing Big Boss during the 1999 incident.
3. He ends up dead in the lead up to the 2005 incident, like Donald Anderson and Dr. Clark. Behind the scenes, that incident was really just a way for Ocelot to cross a bunch of names off his list. Being Big Boss's enemy is a great way to end up on that list.
On the other hand:
1. Interviews suggest that the Phantom Pain is when we're going to see Big Boss getting more and more extreme - I suspect that Miller and Ocelot (two of Big Boss's most trusted men) are performing the torture under orders. All the torture and executions may be part of an effort to flush out traitors in MSF following the loss of Mother Base (I'm actually surprised something like this isn't in Peace Walker, since personally executing traitors was something Che was well-known for).
2. Miller helping FOXHOUND take down Zanzibar Land is actually beginning to look kind of strange in light of what Miller was like in 1974, when he was all about the mercenary business and was super on board with building a Metal Gear. Phantom Pain might see him go through an extreme paradigm shift, but if the foundation of Outer Heaven is in this game, I would be surprised indeed if he doesn't have a hand in it. It's possible that when he was with FOXHOUND in 1999, he was a spy, just like Gray Fox was in 1995.
3. It's still strange that Ocelot and Liquid would have him killed in 2005, since he's almost certainly not a Patriot even if he does end up fighting Big Boss. It could be personal, since it's looking fairly likely that both Ocelot and Liquid will interact with Miller directly in Phantom Pain. It's also possible that it's more infighting between Big Boss fanclub members, like what happened between Gray Fox and Ocelot, and between Big Mama and Ocelot.