Much worse than simply failing to catch Snowden.
First of all, somebody planted the rumor that Snowden was aboard the plane. CIA/NSA picked up the rumor...now whoever planted the rumor has valuble info on the goings on of US intelligence services. Secondly, forcing down Morales plane inflamed anti-American sentiment in Latin America...our reputation there was already shakey. Latin America is a fast-growing economic powerhouse...if the US gives them the middle finger they are all too eager to do business with our economic rivals Russia and China. Really dumb. Lastly, after persueding the EU countries to do our dirty work, we left them hung out to dry. US remained silent while those countries scrambled to CYA. An extremely awkward position to put them in. They may be far more reluctant to cooperate in the future.
In short, I don't think it could have gone any worse. Major fails in many areas of foreign policy. Whoever was calling the shots is a buffoon.