Is there a word for the assumption that a sufficiently complex and refined organ must be the result of natural selection on a large time scale?
The 'term' you are looking for is actually gradual change or gradual evolution. If you want to make clear that this is an assumption or a theoretical consideration, you could say assumption of gradual change or theory of gradual change, replacing change with evolution if you like.

The idea comes from Darwin directly and was challenged in the 1970's by biologists like Stephen Jay Gould that suggested that evolution is not driven by gradual accumulation of changes but rather by morphological equilibria disturbed by many rapid adaptations forming new species, a concept called punctuated equilibrium. 

It speaks for itself that these concepts are opposing but not mutually exclusive. They are rather two extreme states in a continuum.

Edit: As pointed out in a comment by Daniel Weissmann gradual changes also occur in neutral evolution; this is what we call accumulation of mutations - in fact, it also applies to (at least slightly) deleterious variants, especially in populations with small effective population sizes. This means, that the concept of gradual evolution can be generalised to neutral evolutionary processes. However, it does not mean, that the process involving natural selection cannot also be described by gradual evolution. You just have to specify what you are actually talking about. When talking about obviously complex adaptations, you would assume that they have not evolved neutrally.