Because Cupid says they hated each other before heaven stepped in. Dean and Sam had to be born, that was the prophecy, it didn’t matter to heaven how these people felt, or what happened to them, just that they had these two boys.
Heaven certainly didn’t care that they had made these two, with all their differences and all the times they had butt heads, love each other so dearly, so entirely, that they would give up anything for each other. That Mary would give up Sam just to have John. That John was so obsessed with vengeance in Mary’s name that he damaged his kids so entirely and, the worst part, wittingly, yet he turned a blind eye.
Heaven didn’t care what putting them together did to them.
Maybe they weren’t soulmates, just pawns in heaven’s game, much like Dean, like Cas and Sam and everyone else who died because of the apocalypse. Maybe they were supposed to meet other people and live long, happy lives, having other, normal, children that weren’t put to exceeding high standards by a prophecy as old as time, written by a very misguided father. Maybe they weren’t supposed to know the pain of loving one another, the pain of losing such a love, and the pain of blaming themselves for what happened to the products of that love.