The entire point of the relationship is that Newton (the person who destroys systems) gives Anathema (the person whose every thought, action and decision since childhood has been dictated by the cult-like structure of her family) the confidence to break free and make her own choices.
In the book, Anathema’s inner thoughts show that she doesn’t even find him remotely attractive when they meet for the first time, but she just literally shrugs it off and fucks him anyway because that’s what the prophecies say and so that’s what she must do. It never even occurs to her not to do it, because her entire life has been shaped by the prophecies.
If the prophecies say she has to do something, she does it. If the prophecies do not say anything, she focuses all her attention on studying them anyway just in case. She is utterly and completely dependant on them.
And then she finds Newt. A guy who, in the book, is described as not opposed to believing in God, per se, but unwilling to commit before first having a chat with Him. The guy whose entire existence is the embodiment of the cog in the machine.
She starts growing fond of him for real when he shows himself to be supportive, encouraging, and 100% has her back even when it could fuck him over. In the epilogue, he has fallen hard for Anathema, and she is going to marry him because she thinks the prophecies want her to. But, knowing full well it could sink the relationship (the only one he has ever had), he asks her the question nobody else has ever asked her in her entire life. “Are you sure this is what you want?”
Newton was the very first choice Anathema made for herself in her entire life. In that moment, in that place, for the first time ever, she trusted herself with the unknown and took a chance.
I understand the distaste for the “boy and girl fall in love at first sight” trope, as it so often goes hand-in-hand with compulsory heterosexuality. Two people of the same sex have fantastic chemistry and shared backstory, but then they end up married to some person of the opposite sex they made eye contact with once.
But in the case of Newton and Anathema, the whole point of their relationship is “break the system and take a chance.” It’s no coincidence that Neil Gaiman, who fully supports the queer community and has made a career out of breaking harmful expectations, thinks it’s a very sweet relationship.