Structurally, yeah, obviously they're very different.
However, thematically, they share a lot of similarities.
In The Drumhead, Starfleet begins a witchhunt to track down a suspected spy they believe is working with the Romulans.
Into Darkness involves a group of people who attempt to manufacture a war with the Klingons, whom they perceive as a fundamental threat to the Federation.
Both examine racism, fear, and xenophobia in the context of the Star Trek universe, and the lengths people will go to if they feel they're morally justified based on those perceived fears.
Well, I can tell you're open minded and not too critical. I'm sure continuing this conversation will be incredibly productive and enlightening...