If she was not going to get to sleep then damnit, she was going to enjoy being awake at this godforsaken hour of the morning. "Unless your still recovering from your mission, in which case maybe just double checking." Hey she wasn't inhumane and the guy was sporting a rather extensive collection of bruises.
She didn't say anything cliche or cheesy like; 'well don't go away again' because they both knew in a few days (possibly few hours) she'd be grinding her teeth and asking him when he was shipping out again. She never meant it when she asked that, it was always just heat of the moment. It was a shame that they seemed to always be in the middle of a moment - it was always going really well, really badly, or someone was putting their lives in danger. She heard middle ground was nice, but she hadn't ever been able to find her footing there.
So she just kissed him back. Enjoying this moment.
"Never let it be said that SHIELD doesn't train people in efficient pants removing maneuvers. Although I think you already had that skill before SHIELD, hmm?" She teased after he got his belt off (in record time) and dealt with the button. Mind you, in most of her her experiences with SHIELD the quick costume change was because she had to ditch bloodied / dirty clothes, or clothes with bullet holes or SHIELD insignias to switch into less conspicuous clothing. Only with Clint was there ever disrobing of a fellow SHIELD agent for anything else.
Taking a hold of the belt loops she pulled down, helping him remove the pants completely, not lingering to look at the scars on his legs where his legs had gotten broke. That was old damage, and yes scars that Bobbi had poked at before demanding to know the why and how, because she was like that. It was fine for her to have secrets but it drove her nuts when anybody else had secrets.