Nadia is a Widmoreperative: she was in London, where Widmore lives, in Greatest Hits, and was spying on Locke in California. Either Bakir was ordered to kill Nadia because she had "gone rogue", or they were former lovers, and he killed her because she had fallen in love with Sayid. Bakir appears at Nadia's funeral - why would he go to the funeral if he had no relationship to Nadia other than as a target chosen by his boss?