UPDATE 20th June 2019: Sega has been in touch to say it still owns the Alpha Protocol IP, and to clarify the game was pulled from Steam due to the expiry of music rights.
Last night, Sega issued a statement saying Alpha Protocol was removed on Steam "following the expiry of Sega's publishing rights". This was incorrect.
Sega didn't expand on its statement about the expiry of music rights, but it probably has something to do with scenes like the boss fight in the video below, which includes Turn Up The Radio by Autograph. Given Alpha Protocol is nine-years-old, re-licensing music for the game probably didn't make much sense to Sega.