There was no justification to deny the flight passage. The nations in question had no explicit proof Snowden was on board, and acted only on suspicion. This is only an example of paranoia. The flight was stranded in Austria for thirteen hours. The plane was searched without permission. There was a denied request for fuel, even. This overstepped the boundaries of any reasonable actions.
This is the head of state of a foreign government. What self respecting government acts this way? Dirty, dirty pool, old chap. It's like the U.S. Is on a drinking binge. Hopefully we'll pass out soon and wake up tomorrow with a hangover and no memory of what we've been up to of late. Meanwhile, we should probably go outside and wait for a cab to take us home.
America of course has the right to seek out Edward Snowden for his crimes against the US. Regardless of whether or not you respect Snowden or his actions, it was a direct act of espionage against the American government, and he knows this. However, this does not automatically grant America jurisdiction to extend their reach internationally in his pursuit. Morales is the head of state for Bolivia, and as such he has the right of passage back to his country, especially when suspicion of Snowden hiding on his plane was unfounded speculation. There was no adequate reason for him to be held up or delayed purely on the chance that the US could apprehend a fugitive who had left the region of American authority.
The US government will pay for their world wide strong arm tactics in the political, military, and international banking realm. The executive branch will implode within and the people of the Union States Project will have the lawful government in place starting at the Articles of Confederation. Matk my words.