A drone strike or other ways of covertly assasinating Snowden always felt like the trope USGOV should follow if this was an action movie, but it doesn't make much sense in the real world. Mysterious death would only piss off the public even more, and right now the situation is perfectly OK - Snowden is marginalized and harmless. He lives in a far-away land, whatever damage he could do he has already done, no government will ever let him near any data again - he's just a John Doe with no relevance to anything. Not pardoning him keeps it that way.
