You definitely did the right thing in separating them. My two dwarfs lived together for about two months until I decided to split them up, it killed me to see them fighting and unhappy and it made me sick with worry. I don't even think they cared that they'd been separated, they were much happier. Just tell yourself they did the right thing and that they're happier now
And as for pet shops, when I bought my pair the woman told me if they fought I should bring them back and swap them for another pair (like that was ever going to happen, they'd just throw them all back into the same cage and god knows what would happen).
Looking forward to seeing how the two get on with their taming now