how do you know to which miner you're locking the coins to?
You don't. Any miner can claim it later.
You are free to send coins to addresses like bc1qqph8gusf2x7ch4xjs8vnp7hy449r929wnv5jggmy678gam85l6rqgajus9. It has "1000000 OP_CHECKLOCKTIMEVERIFY OP_DROP OP_TRUE" script, so it can be claimed after a block 1000000 by any miner.
We'd need a mechanism to lock the coins in a way the coinbase transactions of a block can spend it.
It already exists, and it is called "transaction fee".
The question would be how the fees can be transferred into a coinbase transaction.
They already are.
merged mining would be an alternative, but it would disconnect both tokens as they would live on different chains
There are ways to use Merged Mining, without forking the chain. P2Pool did it in the past.
which could lead into a slow death of the token (see Namecoin)
NameCoin implemented Merged Mining in a wrong way, because it is possible to do 51% attack on NameCoin, even if you cannot do 51% attack on Bitcoin. They should trace the heaviest chain of double SHA-256 headers, and calculate the global difficulty, based on that. Instead, they have their own difficulty, which is one of their mistakes.
Edit: Not to mention, that they created their own token, out of thin air, even though there was no need to do so. Instead of generating 50 coins in the coinbase transaction, they should create 50 domain names, as it was suggested in BitDNS topic. They should not release any new coins at all, because a payment system was not their designed goal. They wanted to replace DNS, so they should have only domain names in their chain. And they should support buying domains with BTCs, instead of forcing everyone to exchange BTCs into NMCs.
Also, in practice, NameCoin was made obsolete by vanity addresses. Why would you care to buy a name on some blockchain, if you can send someone your public key, some miner can grind you the name you want, and you can pay in BTCs for doing that? And also, it costs zero additional on-chain bytes, because you just replace your random public key, with some grinded public key, and then you have your grinded name, while also having the rest of your address, as some kind of "instance ID", which makes it possible to claim the same name by different coin owners, while also having unique identifiers.