When has Sherlock not treated Molly like she’s brilliant? Honestly, he seems to hold her in very high esteem, all things considered.
I’m not even talking about the “you always counted” scene. I’m just talking about their regular interactions together. While Sherlock must have enough contact with Stamford at Barts to have a conversation about flatmates, Molly Hooper is the ONLY person we regularly see him interact with at the hospital. Is this because he likes to exploit her crush on him? No, because Sherlock wasn’t even aware of it until “Scandal”.
Let’s break down the scenes in which Molly and Sherlock appear together in a professional capacity (so putting aside the Christmas scene):
Pilot / A Study in Pink: Sherlock is actually trusting Molly to give him accurate test results. Sherlock is a very hands on guy. He likes to do experiments himself. He’s got to wait twenty minutes for the bruise patterns to develop on the corpse and he’s got other things to do, sure… But he’s not leaving Barts. He’s looking in a microscope and finding a new roommate. He could have easily set an alarm to check on the bruise patterns himself. But he thinks Molly will be able to give him accurate results.
The Blind Banker: Okay, this episode, he’s just blatantly using her. Molly is in charge of the bodies, he needs to look at them.
The Great Game: While most of the scene is focused on “Jim is GAY”, Molly is coming in as Sherlock is getting test results, asking him how it’s going. While not entirely clear, I think this scene Molly was serving in a similar capacity as in “The Reichenbach Fall”. Sherlock is doing work in the lab and she’s helping out.
A Scandal in Belgravia: Molly is helping Sherlock with the X-Raying of Irene’s phone.
The Reichenbach Fall: Sherlock very BLATANTLY goes to get Molly’s help to examine soil samples.
So we’ve got to ask ourselves, from an in-story perspective (ignoring the fact that the writers just love Louise)… Why is Sherlock always getting Molly’s help? In three of the above mentioned scenes, it literally is not Molly’s division. Molly works in the morgue. Only twice in the above is there any sort of corpse involved in the situation. Twice it’s doing trace samples and once it’s examining a phone, of all things.
Is it because Molly is the only person who will work with Sherlock? I doubt it. Sherlock may be a jerk, but he can be very manipulative (and he must have some sort of pull at Barts to be able to do what he does there, I’ve always fanwanked it as Mycroft influence). Also, if Sherlock didn’t want Molly around he’d tell her. This is a man who told Anderson to turn around because his face was putting him off. If Molly were pestering him, this is a guy who’s not going to hesitate to tell her. He might soften it with “needing to concentrate”, so he wouldn’t burn the bridge of working with her in the future, but still… If he didn’t want her around, she wouldn’t be there.
Okay, so I lied. I do have to bring up the “you’ve always counted” scene. Because this scene proves all of the above. Molly means a great deal to Sherlock. I really feel it was plot contrivance that lead to her not having a gunman on her (and we can fanwank it that Moriarty just underestimated her). Sherlock seeks Molly out to help with his work, because he trusts her in a way he doesn’t others. John Watson is the only one who compares. Even Lestrade is a professional (or a Mycroft-induced) necessity. Sherlock brings Molly into things.
While this is only tangentially related, I think it’s also important to note: Sherlock is never intentionally mean to Molly. While he does say horrible things to her, all of it can be chalked up to the fact he’s a social moron. He dismisses her date proposal because he doesn’t realize she’s asking him out. He honestly believes that telling Molly that Jim is gay is kind (look at the look on his face when she runs off. He has absolutely NO clue why she’s upset. He’s a puppy who’s been scolded from bring a dead animal into the house as a gift). The Christmas scene is a bit trickier. He does mean to say everything he does. He just doesn’t realize the meaning of what he’s saying. But if you listen to the sound of his voice, Sherlock is actually rather friendly. He’s trying to tease her. He doesn’t mean to be cruel. He’s attempting a bit of socialization he’s no doubt witnessed from John, Lestrade and others. Only he goes to far and doesn’t grasp the truth of the situation. When he does, he’s actually pretty horrified. He’s hurt Molly. And this scene is cited often (even by Moffat himself) as the Grinch’s heart growing three sizes. This is Sherlock gaining some of his humanity. This when Sherlock really starts to be more of a good man, rather than just a great one. Even Lestrade and John receive more intentional barbs towards them than Molly does.
Say what you will about them as a ship, but Sherlock respects Molly greatly and I think– save for Watson– she’s the character that brings him closer to humanity.