Bail Organa was killed when Death Star v1 destroyed Alderaan. But before that, did the Empire (or, Vader) ever learn that Bail Organa was working for enemies (Jedi and Rebel Alliances)?
No information yet as of 12/2014.
Legends (EU C-canon) - Yes.
Major spoilers for "The Force Unleashed" ahead!
In the Force Unleashed (mostly-C-canon computer game), Darth Vader's secret apprentice Galen Marek had an assignment from Vader, to lure all the potential rebels into the open, under the pretense of creating an alliance to destroy the Emperor (and in reality, to flush them out and crush them), during the signing of Corellian Treaty in ~2 BBY.
Vader and stormtroopers arrested Bail Organa, Mon Mothma, and Garm Bel Iblis, and took them to Death Star I to meet the Emperor and their doom.
But Galen Marek switched to the Light side, and at the cost of his own life bought the escape of the leaders of the soon-to-start Rebellion.
What really bakes my noodle is, why didn't Palpatine crush Organa in between 2BBY and Alderaan's destruction as per EU.