He wasn’t in love with her. People can feel sadness about losing other people without being in love with them. Sherlock was sad because, for once in his life, he met someone who was his equal (or, at least close to being his equal— the closest he’s ever encountered) intelligence-wise… just to have her die. He wasn’t sad because he was in love with her— he obviously wasn’t— he was sad because, for once in his life, he didn’t feel so alone. He didn’t feel like a freak, because there was someone else who was like him.
Imagine what it feels like to be Sherlock Holmes. Imagine what it feels like to spend your entire life feeling out of place— knowing that you’ll never quite fit in with everyone else. It’s really quite a lonely existence.
That’s why, after examining what he thought to be Irene’s dead body, he asks Mycroft, “Do you think there’s something wrong with us?”
Because Sherlock, as arrogant and showoff-ish as he may be about his superior intellect and deductive skills, realizes that maybe these things that make him different aren’t exactly good. He always wonders why he had to have these skills— why couldn’t he have just been ordinary, like everyone else?
So, that’s why he’s sad when Irene “dies”— because he finally found someone else (besides his brother) who was like him—he was finally no longer alone— only to have her disappear. He was sad, because he was alone again.
“Alone is what I have. Alone protects me.”
^ Fucking this.
Can you imagine living your entire life without ever meeting someone who was your equal (on, at least, an intellectual level? It would be entirely isolating. And then you finally meet someone who can keep up with you, someone who presents a challenge. Even though you don’t like this person all that much, for the first time in your life, you’re not alone.
And then, as quickly as they came, they’re gone. You’re alone. Again. Probably forever. You’ve lost all hope at ever finding someone who can keep up with you and present a challenge. And even though you didn’t particularly like them, you have to mourn them. Because they’re the only person you’ve ever been able to relate to. It’s like loosing a part of yourself. It’s realizing that even people as clever as you are not invincible.