This is the relativity of moral decisions and the only way out is to try to define morality in absolute terms, which has resulted in many religions and philosophical works. The purest (i.e. simplest) form of a moral framework is that of Jainism - it promotes full restrictions on all forms of violence except when necessary for survival (e.g. a farmer killing a farm animal to feed his family).
This may seem like common sense, but it helps that it's defined in a simple form. This is why we don't agree with Tsarnaev or terrorist groups - what they do is not necessary for survival, it serves other purposes. This is why we sometimes just as easily don't agree with president Obama's choices. It has nothing to do with "proper channels", "authority" or any of those words.
Obama has been given the authority to kill along the officially legislated channels of his office. So, there is the distinction: Dzokhar Tsarnaev had no authority to do what he did. What he did was also clearly immoral.
President Obama has the authority. What he's doing is questionably immoral. It's also not the only thing he does that affects people in a material way good or bad.