On your first point; I was matching the behaviour of the C++ program in the blog post, which allows any number of command line arguments but only uses the first two.

On your second point, I actually thought about writing the whole thing as

  getArgs >>= \a -> readFile (a!!0) >>= writeFile (a!!1) . unlines . sort . lines

but decided that that's exactly the kind of thing that gets Haskell programmers a bad reputation.

Agreed, it does and you made the right choice. But in reality once you know Haskell - bind is a very common operation and reading this version is very natural.