Desmond wasn't ignorant to how he behaved whenever he felt any space form between he and his wife. Even if it was space he made up while overthinking, it was space nonetheless.
He knew he burdened her with his thoughts yet she never once told him to hold back and behave.
While she had certainly denied him a few times, his nonverbal begging was normally met with a yes.
She asked him to kiss her and he selfishly wondered 'To what end?' as he lowered himself and their lips met. However, he would be understanding if there was nothing else and they stopped at a kiss. If she didn't express her reasoning, it wasn't his job to figure it out.
He respected her boundaries just as she respected his when they were only beginning and she didn't push him to reveal himself. Even if she was curious, she read him well and knew when to stop. It was the same in their intimacy. Body language was equally as important as spoken word.