Module#prepend doesn't look too bad from me from a complexity perspective - inheritance in Ruby boils down to two parallel trees: One of the inheritance chains, and one of the method lookups. Really we're dealing with a single tree of "actual" inheritance, with some of them being "hidden" in some contexts. It gets a bit complex if you want to do meta-programming or do something that depends on the inheritance hierarchy, but mostly it behaves the way people expect in regular use.
Refinements, on the other hand, looks brain-damaged to me. I see the rationale, but the outcome looks more complicated and error-prone than the situation it is trying to address...
And it looks like the type of thing that will "infect" other code, just like C++ code for a while got infections of throw specifications on member functions, that then got propagated all over the place and cause major pain every time you tried to modify code. Until most people stopped using them much again except in very limited circumstances.