I wonder if Walter and Paige were both hoping / expecting the kiss to be disappointing so that their “attraction” / “feelings” for one another would be easier to manage on a professional level. But when it happened, it was like nothing they experienced before, and they pulled apart because they both knew if they continued, they wouldn’t be able to stop. 

Which, in the end, would destroy the theory of their feelings getting in the way of Scorpion. 

And then, when they were by themselves, they realized just how hard it was going to be to keep a lid on their feelings and act like professional colleagues.