I don't think there's much of a benefit to merging split chains in the current implementation, since both sides of the split probably contain all the same transactions. Even if you were able to deduplicate transactions and resolve any double spends, you'd still have to store the extra copies forever in the blockchain. Where I think this gets more interesting is in a possible future where you don't expect all nodes to receive all transactions.
Maybe this could happen for performance reasons. The network could become so large that no one can handle the volume of transactions. Then we could partition the network into Blockchain USA and Blockchain Europe, or whatever. Transactions would be broadcast only to the partition they originate from, but the blocks themselves could be merged later into a single transaction history. I don't know how much savings we can really expect if we still have to transmit all blocks to all participants (since those blocks just contain the original transactions we decided were too much). But maybe they could compress better? And it might reduce the transaction volume that thin clients have to deal with?
Or maybe this could happen for distance reasons. If some people on Mars start using Bitcoin, they might be as much as 20 light minutes away. With that time lag, they could send transactions, but they'd never be able to mine blocks, and their confirmation delay would be ~45 minutes. But if we created Blockchain Mars, they could have quick confirmations for Mars->Mars transactions, and they could participate in mining with their blocks merged later into Blockchain Earth.
I suppose in such a setup you'd want the average-of-10-minutes-per-block difficulty adjustments to be done within each partition, so the difficulty of each network could end up being different. Not sure how you'd handle mining rewards in that case. But when a block merges multiple parents from different chains, you could count them all towards its difficulty for the purpose of determining the longest chain.
I'd be curious to hear people's thoughts.