I doubt they knew he had a secret role - there was no such evidence in the thread, and a night-spy power that returned before the murder decision had to be made seems pretty overpowered.
That said, this seems like a classic WIFOM - either they killed a low rank to promote one of their own, in which case there’s a one-in-two chance of lynching scum on the first day and a dead-cinch lynch on the second (if you accept scuba and chronos’s claim), or they killed a low rank to cast suspicion on the three lower-ranking players so as to arrange a series of mislynches, in which case there is a 0% chance of lynching scum, and if you follow up and lynch the other one tomorrow you maybe end up handing the game to the scum.