A/N: When I use the word "love" here I'm referring to love between friends, since Sherlock and John have the most epic bromance, but I don't think they're in any sort of romantic relationship. However, if you are a hardcore Sherlock/John shipper, feel free to use the romantic interpretation of "love" if you wish.
On a literary note, I know Mephistopheles actually tried to dissuade Faustus from exchanging his soul for knowledge and riches. I think that Sherlock was seriously considering taking Moriarty up on his offer, and if Moriarty had used anyone else besides John as a bargaining chip, Sherlock would have done so. However, by using John, Moriarty showed Sherlock just how callous and evil he really was, which actually caused Sherlock to reject Moriarty. So it's kind of an inverse of the character; Mephistopheles tried to get Faustus to choose the good and Moriarty tried to get Sherlock to choose the evil. Both of them failed, in the end. I don't know if I explained that clearly, but hopefully you understand that I'm not being ignorant of the characters in Faust.
Summary: Jim Moriarty is not just any old devil.
"Alas, I have studied philosophy,
the law as well as medicine,
and, to my sorrow, theology;
studied them well with ardent zeal,
yet here I am, a wretched fool,
no wiser than I was before."
- Goethe's Faust
"No, if you don't stop prying... I'll burn you. I will burn the heart out of you."
"I've been reliably informed that I don't have one."
"Oh, but we both know that's not entirely true, now is it?"
Sherlock understands now. It's a trade-off. Sherlock's 'heart'- his flatmate, his only friend- in exchange for his career, his passion, his life's work. Or vice versa. Could he do it? Could he sacrifice John for the opportunity to play Moriarty's little games?
It's not outside of the realm of reason. Because Moriarty... Moriarty is special. Moriarty is breathtaking; never has Sherlock met one whose mental faculties rival his own. Here is someone else who staves off boredom by reveling in the blood and filth of criminal underworld. They are perfect mirrors of each other, and Sherlock can hardly tear his eyes from the image.
And John... who is John? A dull pedestrian with a funny little brain. And yet, he is so much more. It doesn't make sense. John doesn't make sense. A wounded veteran who, upon returning to a peaceful civilian life, immediately jaunts off with a sociopathic consulting detective. Who the hell does that? John even saved Sherlock's life on their first case together, before Sherlock ever thought of John as anything more than an assistant who conveniently also happened to help with the rent and make tea.
He had said something to John during their first case. "Love is a vicious motivator." What does Moriarty love? Power, most likely. Anything else? Sherlock's eyes rove over the other's face, taking in black eyes shining with cold glee; a small, smug smile; the expensive, well-pressed suit. Pain. Moriarty loves seeing others in pain. He loves holding all the cards, stamping others underneath his polished shoes, being the one in control.
Sherlock loves his work. He loves straightening out all the jumbled little pieces, loves the looks of uncomfortable amazement on others' faces when he deduces things they would never be capable of seeing. He does not love the feeling that he has done something good or heroic, because he solves cases for his own pleasure. He thinks that there is some part of John that loves the thrill that comes with investigating cases, but John also loves taking dangerous criminals off the street. John most certainly loves Sherlock, and Sherlock thinks that he might, he just might, love John too. He trusts John in a way he could never trust Lestrade, confides to John things he could never tell Mycroft, overlooks John's flaws in a manner he could never overlook Anderson's.
And this is John's advantage. John can love Sherlock, can speak to him, counsel him, make him watch bad (but secretly entertaining) telly. What case can do that? Moriarty doesn't hold a candle to John, in that respect, because Moriarty cares only for his power and his greed. Moriarty is brilliant, yes, but he is also cruel and calculating. If Sherlock chose to play his games, the two of them could drown the world together but they would eventually go down with it, pulled by the weight of their hatred, bound and gagged in their competition.
He cannot let Moriarty take his heart. This game, he decides, is finished. No deal. Let Moriarty go his own way; Sherlock will bring him down eventually. In the meantime, Sherlock will be content to keep his heart, his John, safe with him on Baker Street.
He lowers his gun, and hopes he has made the right choice.