Well, I'll try to explain...
How much work would be involved in setting up NASSP as a stand-alone programme. Is everything written in a way only Orbiter would understand?
NASSP is written as an Orbiter add-on, that means it uses Orbiter's physics and graphics engine as any other add-on. To get rid of Orbiter, well, you'd need to re-implement that stuff, which would be a re-implementation of Orbiter itself.
...and put it into an engine that only simulates the earth, stars and moon states (as opposed to half the milky way) and which will make it easier to get more historically accurate orbit parameters
Orbiter does not simulate "half the milky way", but the solar system. If you want to use only Earth, Moon and the Sun as gravity sources, just throw the remaining bodies out of Config\ProjectApollo\Sol[_VirtualAGC].cfg, no need to switch the engine. Also, you're certainly aware of that the real missions took place in our solar system including all planets (no offense, I'm just not sure how to explain it...), so if you throw out planets, the simulation gets less precise, not more.
I just ask because I see a lot of comments about being unable to completely replicate the original missions because they can't replicate the exact same orbit parameters...
I'm not sure which posts you're referring to, but I can't imagine this is because of Orbiter's physics engine, which is pretty good since we have non-spherical gravity sources etc., but because of inaccurate simulation of the spacecraft (for example only the Apollo 7 and 11 Saturns are using correct parameters at the moment, i.e. a NASSP problem, not Orbiter's), unsuitable navigation tools (see here for example: http://www.ibiblio.org/mscorbit/mscforum/index.php?topic=2706.0
) and user errors.
...can't implement ground control read-up of PADs, etc...
I'm not aware of that Orbiter is a problem in any way for implementing ground control stuff?
(But I am aware of that our very limited development resources prevent that at the moment...)
Concluding I don't see any sense in getting rid of Orbiter, but perhaps I don't understand your question correctly?