I'm gonna have to go all cynical and pick answer #2. Remember, Gates was in Bahrain the day before the Saudis and UAE sent in troops. There's no way that they didn't mention this to Gates beforehand. I think the prospect of a Shi'ite revolt which puts a (tentatively) Iran-friendly government in charge of our biggest US Navy port in that part of the world.....just not strategically acceptable to the Pentagon (and probably not to the WH).
Of course, I've always been of the opinion that hey, if you actually stay out of the way instead of working to suppress them, they're a lot more inclined to be favorable to you later on. We found out the hard way that a lot of "socialist"/left-wing governments that we suppressed during the Cold War actually hated the Soviets and would have preferred to deal with us.
EDIT: Starting to see some resignations in the Bahraini government over the crackdown. 2 ministers, 8 members of the Shura, and about a dozen judges so far.
P.P.S: Interesting analysis from
Foreign Policy: The Bahraini military (about 30K strong) is apparently loyal to the King and Crown Prince, who are known to be fairly liberal for Arab monarchs and who have expressed a willingness for reform in the past. The police, security forces and other assorted paramilitary and law enforcement in the country are roughly equal in size to the military (and are composed mostly of non-Bahraini Sunnis) and are loyal to the Prime Minister, who is a conservative who has dismissed calls for reform. The Saudi/UAE presence may be there not so much to guard against the protesters as to tip the balance of power in the event of a showdown betweeen the throne and the Prime Minister. This actually wouldn't be without precedent -- I seem to remember certain German states that were in the same sort of situation during the Liberal Revolutions of the 19th century.