I think we need to establish the mass of the incoming neutron star. I was assuming a normal neutron star (NS), i.e. something like 1.5 M
solar. A less massive one would not be physically possible since the matter will not be degenerate any more and free neutrons decay very quickly (half-life of 15 minutes or so) into protons.
Such a significant short-term change in the matter distribution of the protostar system would likely have catastrophic consequences for the gas disk. These things are not very stable to begin with, being very turbulent due to a wide variety of gas interactions. A strong magnetic field might do
something, but probably nothing good.
I don't think rotation will affect anything at all. Rotation only has an effect on gravity in extreme cases (see
Kerr metric), but I haven't done any GR so I can't really comment. Since your average NS does not have much more mass than the sun, (and in fact, neither does it have more angular momentum) rotation would not have any effect on stuff orbiting it.
Orbiting retrograde would not really do much for the NS at all. A retrograde orbit around something else is perfectly stable, many of the solar system planets have smaller moons that orbit retrograde and they are on perfectly stable orbits. There's even one major moon,
Triton, moon of Neptune on a retrograde orbit. Tidal effects are causing the orbit to decay due to being very close to Neptune, however, so on very long timescales (3.6 Gyrs) Triton will
crash into be ripped apart as it enters Neptune's Roche lobe.
Anyway, even the gas will probably not slow down the NS enough to make it merge with the protostar, having a mass of only ~1% of the protostar itself. In astrophysics everything is a question of mass and time. When you have a large mass difference and a short time, the little guy is in for some serious changes to his way of life. So to speak.
The NS
will at some point merge with the no-longer-a-protostar (at that point probably a white dwarf), at some point due to them emitting gravitational radiation. This takes a
long time, however, quite probably longer than the current age of the universe, depending on their initial orbital separation and eccentricity.
It would also depend on how far out the degenerate matter clump was orbiting the protostar. (Is it orbiting the protostellar object's core mass, or the combined mass of the protostar and planetary disc?)
Finally, this piece is a bit weird. Something outside of the protoplanetary disk will always orbit their combined centre of mass. The combined centre of mass will be quite close to the protostar's centre of mass anyway due to the disk's low relative mass.
Heh, this got a bit ranty, sorry for that.