Wait... I've been confused about this whole conversation since I saw it.
Possibly the "I don't think so, do you?" line was just said weird. Reading it now it makes sense... but when she says it the emphasis just sort of makes it odd.
But here's the thing- Irene says she's gay? 
I have 2 problems with this line.
Firstly- She could have been replying to John's exasperated comment about no one being sure what or how Sherlock thinks or flirts or his sexuality. (PROBABLY not true.. but interesting to think about)

Secondly- a gay woman wouldn't get dilated pupils and an increased heart rate from a man. She also wouldn't have a school girl crush on him and change her phone password to his name. The phone could POSSIBLY be just an obsession with his intelligence or something, but the physical reaction to his touch/presence is something that can't be faked. Heart rates can be manipulated internally sure, but eye dilation? And if it was manipulated then there would be no obvious connection between her physical response and Sherlock's conclusion about the password.

Are we sure she's gay? Something doesn't add up.

Ah.. that makes WAY more sense now! hahaha thank you!

Yep.

anjaH_alias wrote:

I think it was meant like "you know, before meeting Sherlock I thought I was gay. I am living together with a woman as you know. But look where we are: You (John) are hetero and now love a man (Sherlock), I (Irene) am gay and now love a man (Sherlock)."
It´s of course not the same kind of love about what she´s talking . John´s love is deep true friendship and her love is a mixture of intellectual fascination and sexual attraction. But it brings both of them in a similar position that time (at the Battersea power station).

 
Completely agree - nothing to add!

I think this is probably the most beautiful scene of this episode or well, together with the "Sherlocked-scene".