Natasha has the bomb almost completely set up when she stops to think. It's in a big enough box that it'll look like someone is asleep when she tucks it under the covers, and it's set to trigger when someone pulls the blankets off. Her plan was to leave just enough time so he'd realize what happened before the little bungalow blew sky-high. His fault for trusting her.
She's not sentimental. They call her the Black Widow, for fuck's sake. It just seems like... bad sportsmanship, perhaps, not to give him a fighting chance. Clay's not very bright, sure, but he's handsome and talented -- is he ever talented; his hands will be a regular feature in her spank bank for years to come -- and really, having him live to fear her could only be a good thing.
She puts an extra 30 seconds on the timer, and thinks of it as her gift to the next woman Clay lives to hook up with.