I really don't think Rachel is the third girl, I highly doubt she would be in good terms let alone a working relationship with people she pretty much betrayed, but there's still the chance for that to have been agreed upon by the three of them I guess.
There's still the matter of Motoko's missing parents, her mother as many thought might be that other girl, and there's also Keiko's boss, whoever it was, who send her to search for Rachel's work, and so on.
...it's a reasonable assumption...
It is, that doesn't mean it can't be a negative one, is like telling someone who's seriously ill "you'll most likely die", is reasonable and not impossible for it to happen, but the comment is still negative all the same.