There's no direct evidence about this, but consider when it happened. The last event before that odd sculpture whacked Nancy on the head was Nancy calling Victor to tell him that his prime frame-up, Ryan, had been conclusively cleared. I don't think he wanted to kill Nancy; after all, Ryan said she was the only one who knew the air would be turned off in that room. I think he just wanted to get her out of the way for a while to give himself time to think. And don't forget, it was after you were locked in the lab that the evidence incriminating Ellie and Mason -- Ellie's cell phone and the missing keycard -- suddenly appeared in the office lounge area.