Newtonian Mechanics: Science or Pseudoscience?

I've read with great interest the discussion here and elsewhere regarding intelligent design and the falsifiability demarcation theories in science.  I was reading David Berlinski's recent article in Commentary entitled On the Origins of the Mind and came across this quote:

This is precisely the problem that Newton faced in the Principia. The magnificent “system of the world” that he devised explained why the orbits of the planets around the sun must be represented by a conic section; but Newton was unable to account for the initial conditions that he had himself imposed on his system. Facing an imponderable, he appealed to divine intervention. It was not until Pierre Simon Laplace introduced his nebular hypothesis in 1796 that some form of agency was removed from Newtonian mechanics.  (emphasis mine)

Some questions:

1. Since Newton appealed to divine intervention in the initial conditions of his theory does that indicate that this part of his theory, and thus the theory itself was unfalsifiable, and therefore not science?
2. Since the nebular hypothesis did eventually replace what Newton originally posited as divine intervention, isn't this an example of the falsification of a theory that used a divine agent?
3. Since the theory of Newtonian mechanics evolved from one that depended on a divine agent for its original conditions to one that did not, did the equations of the theory itself, which did not change during the transformation, change from being "pseudoscience" to science?