You know, the sentence "I cannot pardon Snowden without a trial" does not necessarily imply it is physically impossible. He was saying "I choose to not choose to pardon him"
There is a meaning of this sentence that implies a malfunctioning or misguided proximity-based home security system, probably using Bluetooth. But every time you've heard someone say something like this, they haven't meant it that way.
"I can't eat peanuts."
There is a meaning of this sentence that implies a sophisticated and unbypassable filtration system in front of the speaker's mouth. But every time you've heard someone say something like this, they haven't meant it that way.
Obama's statement isn't unambiguous, but not using phrasing such as "lack the power to" or "Constitutionally prohibited from" carries inferential weight, too.
The meaning of a statement depends on who the audience is.
In your examples, logically they are both lies. But, the meaning that is being transmitted is something more akin to: there some obvious, if unmentioned, reason why an action would be undesirable. And, this meaning is pretty clear to an average person in both cases.
Obama has logically lied. There is no question about that. But of course, we aren't talking about whether he lied, but whether he implied something untrue.
Given his response, "I can't pardon somebody who hasn't gone before a court and presented themselves", it's pretty obvious that an average modern American would at least assume the implied meaning is that something outside of his control is preventing him.
Therefore, your contention that he could have been implying "I can't because I choose not to", could not be correct, since he knew who his audience was, and having decades of practice as a career politician communicating with that audience, knew very well the meaning they would take from that.