Conceptually, it seems that a computation that performs output is very different from one that performs input only. The latter is, in one sense, much purer.
I, for one,
I disagree with bdonlan's answer. It's true that neither input nor output are more "pure" but they are quite different. It's quite valid to critique IO as the single "sin bin" where all effects get crammed together, and it does make ensuring certain properties harder. For example, if you have many functions that you know only read from certain memory locations, and which could never cause those locations to be altered, it would be nice to know that you can reorder their execution. Or if you have a program that uses forkIO and MVars, it would be nice to know, based on its type, that it isn't also reading /etc/passwd.
Furthermore, one can compose monadic effects in a fashion besides just stacked transformers. You can't do this with all monads (just free monads), but for a case like this that's all you really need. The iospec package, for example, provides a pure specification of IO -- it doesn't seperate reading and writing, but it does seperate them from, e.g., STM, MVars, forkIO, soforth.
http://hackage.haskell.org/package/IOSpec
The key ideas for how you can combine the different monads cleanly are described in the Data Types a la Carte paper (great reading, very influential, can't recommend enough, etc.etc.).