You need to use console commands on a PC in order to complete the quest. http://www.gamesas.com/topic/1576764-failed-to-defend-settlements-where-synths-attack/#entry24767012. Basically, you have to resurrect the dead settler (the synth infiltrator) and kill him or her again to complete the quest. The quest won't complete without using the console, sadly. This is obviously a bug, of course. At least this doesn't seem to occur that often. I'm up to level 54 and only have had 2 synth infiltrators.
To resurrect a dead settler, point the cursor at him or her until the cursor turns into square brackets (i.e. [ ] Settler). Press tilde (~) on the keyboard to bring up the console. Left mouse-click on the square bracket cursor, and you see the settler's ID appear. Type the console command resurrect and press Enter. Press tilde (~) again to close the console. The settler should come back to life. Kill the settler and your quest should be completed. You may need to resurrect-and-kill more than once to succeed.