This is not true. Snowden had to fly to Russia and live there for three years before a hypothetical pardon. If that is the minimum for the possibility of a pardon, I don't think many people would find that emboldening.
Spending three years in exile is not great, but it's a far cry from a long prison sentence for leaking classified documents.
Sure, you could try to go "underground" but you'd then become a top assassination target for the worlds most powerful security service. No one would ever know of your assassination either - you'd just disappear.
Obama may be one things, but lying on a political spectrum neatly is not one of them. In fact, it's pretty damn hard finding a president who HAS been straightforwardly liberal or progressive, much less one that played well with the constitution. I'm not sure why you expect those two things to align.
Those potential leakers might be emboldened, but I doubt many would get away with it. There is also a great deal to be said for Snowden being right.
If the President pardoned him while denouncing other named leakers (Manning, et al), and highlighting that Snowden was the only one protecting the constitution. Then perhaps only the leakers strongly backed by the constitution would be emboldened.