The rule is against realm mergers—that is, against one realm effectively ceasing to exist by a significant majority of its lands and nobles transferring to another existing realm.
So, by the rules, the proper result was the death of the realm, not its merger.
The realm's not dead, nor has it effectively ceased to exist. It still has a ruler, nobles, gold, soldiers, and the ability to engage in trade, diplomacy and military action with other realms.
