When should they stop selling ships for real money?

once we reach open beta (maybe full release) there won't be the ships for sale outside of the game and it will be much simpler to earn things in game than buy what little UEC you can with money.

At what point would selling ships qualify as the pay-to-win scenario many of us abhor?

With the REC system in place now this opinion of p2w is misinformed, sure you can donate more to the alpha and get more and bigger ships with insurance but the fact remains that SCs endgame content is basically "become the best Blank in the verse". Just paying money for a ship isn't going to get you there any quicker than the people who spend time on the starter ships honing their skills (infact you'll probably get there slower). Ultimately i think unless your a collector or need an org. base buying more and larger ships is completely pointless. I myself have spent over a thousand supporting this game but it wasn't just for the ships and aside from my orgship i plan to stick with a startership to work my way up in the PU.

The cash model is so good at the moment, do you think they might be tempted to transition straight from funding to an in-game store? (They are a company, and it's not wrong to make money)

They deffinately going to keep some of the cash model, such as subscribers (which funds community content), physical merchandise, and even UEC (in game money) with a cap to discorage gold farming and not provide a distinct advantage in the verse. As for in-game store they are planning to sell cosmetic items so they can still make money but not be a p2w model.

hope that answers your questions...