Molly feels guilty almost immediately because even if she tells him the truth it will still hurt him. He still blames himself for Mary. It's wretched either way.

"It's not you," she says shaking her head and swiping at her eyes. "You've been lovely...I...sorry....I was just thinking about... Mary and...well...I think I'm also just rather emotional right now."

In the past 2 days she's had her feelings laid bare in a horrible way, she's got Sherlock confessing his love to her, they just had some version of sex in her bed, and he's still here and wanting to do...this. It's a lot to manage in a short time.