His heart stops right there. He is staring at Molly; his friend Molly Hooper. The woman who gives him access to as many cadavers as he could hope for. The woman who has often, in the past, brought him coffee after he has been working long hours, always remembering "two sugars, black." The woman who has, on occasion, sat with him and watched him work, sometimes adding a bit of companionable conversation which, much as he loathes to admit it, he has occasionally found to be mildly entertaining (especially after hours with only the dead for company). And here she is, and she is wearing lipstick. Lipstick!
He can't believe it. Were it not for the other subtle clues her body is subconsciously giving off, he would assume it to be a mere fluke of nature. But it is not. Molly was not wearing lipstick before and now she is and there are not too many plausible explanations. Molly Hooper is attracted to him, Sherlock Holmes.
Sherlock, never lost for words, is struck dumb for the longest heartbeat his heart has ever given. She can't like him like that. It isn't possible. She is his friend! What can he tell her? If he refused her advances, she won't understand. She will be offended (and not just the annoyed effect he seems to have on anyone crossing his path). No, Molly will be actually hurt if he were to tell her that he does not fancy her in return. She is one of the few friends he has and if he hurts her, he could very well lose her permanently and that is not a risk he can afford to take.
So he ignores it – the gesture. Pretends he does not realize what it is or who it is for. It is the only thing he can do. If he acknowledges that he understands, he will be forced to tell her that he is not interested in a romantic relationship and that is something he cannot do. Despite his typical complete lack of regard for societal conventions, Sherlock does know that sometimes, in exceedingly special circumstances, there are things that are better left unsaid.
So he gives her his best look of feigned ignorance and returns to his microscope, ignoring the sharp jab her pained expression sends ripping through his heart. 'It was the only way,' he tells himself again. His lack of interest in romance will not cost him his closest friend… not again.