The petition is specifically about pardoning Snowden. The President cannot pardon someone for a federal crime they have not been convicted of. Snowden literally needs to come back, face the trials, and be convicted before the President could consider to pardon him.

To me, the response is a have your cake and eat it too kind of response. They hint at the technicality of not being able to issue a pardon in a way they sound tough on people like Snowden. Rather than "come out and fight like a man", it is "security, security, security, Snowden hasn't been convicted yet, security, security, security".