Actually, I think that a more compelling argument against nanoreplicators (I'm no expert) is space, not time. If you build a billion, you overcome the time problem, but you replicate the factory one billion times.

A separate factory should allow a more efficient nanobot.

Furthermore, a separate factory should enable a better (and larger) factory that is also easier to design, given today's technology.

So I agree that there are good reasons to avoid nanoreplication, but argue that the problem is ease of design second, and wasted resources through unnecessary duplication first.

OTOH, you could design different generations of nanobots, with the early versions containing factories, and later generations containing purely the lean mean efficient machines.