From what I have noticed watching BJ/JBJ shows including some guest female stars, the kiss at the end of the song is simply a kind of procedure. It simply is Jon's expression of respect to the acompanying star and his way of saying thank you.

He thanked betty Lavette during the Obama Inauguration show in the same way. He also kissed Ann Lee Rimes at the end of the performance of "Strangers" when they were performing Live. The same when he was singing on LAte Nite Jimmy Falon show in March 2009 with one of the female fans. Nothing particular or scandallous!