I don't know if it was so much guilt from Jack, as it was more a feeling of concern with Ennis reaction to him the next morning. Jack had guided Ennis through this, that's why Jack "waited" for Ennis to come to him on that hill.
By "topping from the bottom", Jack enabled Ennis to explore this part of him, and by letting him know, "Its nobody business but ours" , "You're not queer, OK fine", "This is a one shot thing, you got it." It was all safety nets.
Jack had to ensure that trust Ennis apparently needed in order for him to go to Jack that second night. It was about trust. IMO.