Williams was unhappy with his work environment at MI6 and felt he didn't fit in with his colleagues. During the inquest, testimony revealed that the coder had conducted unauthorised searches of an MI6 database
also: http://www.wired.com/threatlevel/2010/08/codebreaker-death/
"The source indicated that Williams' work to disrupt the Russian mafia could have put him at risk".
"Some of these powerful criminal networks have links with, and employ, former KGB agents who can track down people like Williams," the source said.
"MI6 did not report him missing, however, until 23 August, at which point his body had decomposed, thwarting attempts to determine the precise cause of death."
His own spy agency failed to report him missing which is pretty suspicious all by itself. To me, this would indicate they're most likely involved. They also left out the fact the heat in the flat was turned up to speed decomposition and the reason the bag was in the bathtub was to make it easy for body fluids to drain.
Lots more details which indicate a professional hit:
http://www.trutv.com/library/crime/blog/2013/01/04/gareth-wi...
It's the British government, one of the most bureaucratic agencies in the world. The fact that the form to notify the police wasn't lost while bouncing around is the only surprising thing to me in that sentence.