It is perfectly normal for two boy buns to act like this when they hit puberty. I’m glad you’re all safe! Your gut instinct is correct, you need to keep them separated until they are neutered and fully healed (1 month is recommended you wait after the neuter). They will be lonely without each other, so it’s good if you keep them where they can smell and hear each other.
Since they’ve only fought once and since they came out of it without injuries (check their gentital areas carefully for wounds, they tend to go for those parts), re-bonding will most likely not be a huge deal since they’ve grown up together and been friiends until now. I would recommend you to not let them meet until they are neutered + healed, because if they fight more, re-bonding will be more difficult.
So, you are doing everything by the book here, and their fighting was not due to something you did wrong, it’s just hormones and boy bunnies being boy bunnies. I don’t think you seem naive. It’s not so super-easy with bunnies since they are a belligerent species, in spite of their fluffy and innocent appearance.