It's worth distinguishing between manipulating a function as an "external" value and making "internal" changes to a function. The first case is completely unproblematic. The second is potentially extremely complex and so far intractable in all but "duh" cases.
To be clear, I'm talking about the former (manipulating it as an opaque value). I've never seen a program (save esoteric Haskell ones) that did anything with functions that even approached requiring Turing-completeness.
