That kind of transaction is actually good! We want to
encourage stuff like that. In fact we've talked about making clients do it automatically.
Here's a quick recap. Bitcoin has two types of costly data storage.
1) The block chain. Someone, somewhere, has to keep every transaction ever made, forever. However, whilst today that means "everyone who runs a full node", in future, it will mean "people who explicitly choose to" and every other node will be a pruning node - old data in the chain gets deleted. One can imagine that in a world where Bitcoin is tremendously successful there will be many organizations will to archive a data structure of such importance. Perhaps the Library of Congress
2) The unspent output set. Every full node has to maintain this, what's more, they must maintain it in high-speed storage. When a tx creates outputs this set grows, and when they claim outputs with inputs, it shrinks.
We can see then that whilst transactions like the named one are quite large, in the distant future only a small number of parties must store it, perhaps even on long term storage like tape drives. However it collapsed many tiny outputs into one large output, which reduces the size of the UTXO set for everyone.
