However, this burdening is something that Bitcoin users and developers will just have to live with. Nobody is the boss of Bitcoin, and any standard Bitcoin transaction (like Mastercoin transactions are) are legitimate transactions that Bitcoin simply has to learn to deal with. There is just no feasible way that I see that Bitcoin developers could ban such transactions (please enlighten me if I'm wrong).
If the devs were able to do this -
http://bitcoinmagazine.com/4465/bitcoin-developers-adding-0-007-minimum-transaction-output-size/ - they can ban Mastercoin transactions. Bitcoin's decentralization is just a myth. All big pool owners will do what Gavin and Co. will ask them to do.