If they pardon him, they say it's alright to release national secrets based on "feelings" (even if it's morally correct to do so, they can't have that). If they try to get him to the US for a public trial, who knows what will happen. If they bring him home for a secret trial, the risk rioting or a martyr. Similarly, if they kill him with a direct assassination he will be a martyr, and they'll be dramatically ruining their image. Finally, if they kill him in a covert way, no one will believe it and in all likelihood it will be widely believed it is the governments doing.
By leaving him in this limbo, the government can claim what ever they want about him without proving it. At the same time, Snowden has no more info to disclose, although he has a solid and growing cult following.
For the record, I signed this as soon as I heard about it and shared it with everyone I knew. I think it's important to be counted and try to share and convince others if your beliefs, if you believe it'll dramatically impact your future.
What Snowden did and what he stands for is the last chance to have any form of democracy or privacy. Unfortunately, it appears to have failed, but that doesn't mean you stop trying to improve things. Perhaps, the younger generation (millennials and below) will recognize what he did, as opposed to what the government is trying to spin.