Earlier quoted context omitted.
Politics is the art of compromise.
Well, from a political point of view, Snowden is just a guy, and he did what he could do already. Pardoned or shot dead, makes little difference now (well, chilling effect is certainly even worse if the latter happened tomorrow, but its bad enough as it is). The important thing would be wistleblower protection laws changes that would protect a future Snowden from this situation.
Law is built on precedent. This is how a two-hundred year old law about papers in one's house was used to try and pry open an iPhone. It is also why people get rightly indignant about seemingly small things.
In the specific context of the data Snowden exfiltrated, you are correct - a pardon changes little. But for the next Snowden? Or the political climate surrounding his "treason" versus "whistleblowing"? Totally different.