If somebody is paying fees to store arbitrary data in the blockchain, just let him be.
First,
Bitcoin is a decentralized currency. It is not a data storage service. Bitcoin would be a very bad design for a storage service, and it's only attractive to some for this purpose due to the non-consensual aspects of it.
As far as fees go— there is no automatic moral righteousness that comes from paying fees: If I pay a big enough fee to your neighbor should I be able to show up and drill holes in your head? Why not?? I paid a fee!!!!
The costs of data storage are not just borne by the single miner that accepts the transaction and has arguably been paid for their trouble they are imposed on the entire network— all current and future users of Bitcoin— for all time. Of course, miners who don't agree with the policy are free to adopt other fee policies— there is even a config file setting for it but I expect that few to none will— because they care about Bitcoin as a currency and want the bitcoins they mine to be valuable.
You can expect that the core development team will continue to defend Bitcoin against non-currency usage at least to the extent they believe and there is evidence that the non-currency usage is non-trivially harmful to the usage of Bitcoin as a decentralized currency. If you don't like it, you should probably find other software to run. (And probably another network: I doubt you'll find many Bitcoin users who are friendly to chewing up their bandwidth, diskspace, and processor cycles to store data that you're not paying them to store)
Finally, even with this change people can still create stupid data bloating transactions— but they need to put as much bitcoin value in their unspendable outputs as a plausibly real transaction does. This is a 5000x disincentive and the result is effectively paying all the current and future users of Bitcoin through increase scarcity.
I agree with you, but it's still sad to see biased behavior being embedded in the reference implementation. It's like bitcoin.org. Not a monopoly, but still, the "reference". I'd very much prefer if it remained the most unbiased possible.
Biased how? As I posted in these threads— Bitcoin is _full_ of restrictions, its value is— in fact— derived almost entirely from restrictions. Discouraging the creation of transaction outputs that yield fewer Bitcoins than they cost to spend is pretty "value neutral". It's a little insane that they can be created at all. As far as I'm aware a policy to restrict them doesn't discriminate against any kind of usage other than the "usage" of forcing hundreds of thousands of machines to archive non-bitcoin data against their operators consent. As far as I know it won't interfere with any publicly (or privately, for that matter) known service. So whats this bias that you speak of? Please— point me to a currency use of Bitcoin that this will break, because if there is one then we need to figure that out! If it's something private, reach out to me via gpg encrypted anonymous email.