So I'm going to open up the discussion and I would like to see arguments for why I should or should not explicitly support merged mining, and I ONLY want to see arguments that don't include "it is more profitable". More profit by "earning" namecoin at the same time as earning bitcoin does not support anything to do with bitcoin as a concept of a cryptocurrency that ultimately makes free trade possible.
Before I respond to it I think it's important to emphasize that there is _NOTHING_ fundamental about the problem here. Regardless of merged mining the bitcoin daemon needs to be able to tell workers that they need to move on to new work— this arises without prev changing due to merged mining, sure, but it is just as equally an issue if a new txn with high fees hits the memory pool, a pool server is simply restarted, or a network failure switches remote miners to another datacenter.
Many people misunderstand merged mining— they think things like it means automatically switching between systems, or that it lowers the work useful work miners do on bitcoin. This is not true (save any software bugs that crop up while adding the feature— but you can say this about _ANY_ feature).
Now, as far as the goodness of MM goes— forget about the profitability of it, it's not why MM is important. Merged mining is a major improvement in the fundamental trustworthyness of Bitcoin:
Prior to merged mining, adopters of bitcoin took the risk that IF bitcoin lost popularity (or, even didn't lose popularity but mining became less attractive due to energy costs, declining rewards, etc) THEN bitcoin would NECESSARILY become insecure— and vulnerable to reversal attacks.
With the existence of merged mining bitcoin being popular or profitable-to-mine is still sufficient for security but it is no longer strictly necessary: Bitcoin is secure so long as the sum of ALL distributed systems which use the nakamoto block chain distributed consensus and share work with bitcoin, some of which may have no "coins" at all, are popular enough to provide enough mining hash power for security.
For example of a very different application: P2Ppool now uses merged mining to achieve consensus about the distribution of payouts for the distributed pool.
Merged mining is also very good for bitcoin because it reduces the incentive for various parasitic behaviors. For example, some people have wanted to cram random data into the block-chain for proving time of creation. This is bad for all bitcoin users because our system fundamental depends on flooding and near global awareness— bitcoin is the least efficient data storage system used by man (short of our own genome). Merged mining would allow these parasitic loads to exist in separate chains. (Importantly, the _only_ cost to bitcoin for merged mining is a single hash in the coinbase, and whatever software bugs miners suffer while implementing it, and MM has O(1) scaling— with one additional hash in the coinbase we can support an infinite number of merged chains)
Also, In cases where a system using the same computing resources becomes as interesting as bitcoin mining you risk hash power oscillation unless you have merged mining. At one point we had a good few hundred GH/s bouncing between NMC and Bitcoin every difficulty change. Because bitcoin was still growing hashpower quickly at this point it wasn't a terrible problem (well it was pretty devastating on namecoin, and only wasn't on bitcoin because bitcoin miners were fortunately slow to respond to the extreme profitability of namecoin). But if the swing had instead been twice as high or happened when we had declining hash power we would have been seeing very noticeable cycles of slow blocks.
It's also the case that you're wrong to ignore profitability. Because the profitability of mining contributes to the attractiveness of adding lots of hash power legitimately which provides bitcoin's security (as opposed to the profitability of using hash power to attack). If you make legit mining more profitable you make bitcoin more secure.
Finally, even in cases where you can argue that MM is bad (perhaps the various scam-coins) you can't actually prevent merged mining. The current system works cooperatively with the binding in the coinbase txn, but you could always bind other hashchains by stuffing the binding hash in a parasitic transaction.
So, I think it's clear that merged mining is technology which is good for bitcoin even if the specific usage with NMC is boring and the software is having growing pains.