Well, the character has been off of the experimental meds that Cerberus was giving her for 3 or 6 years (depending on whether you go by the calendar or by her age). It's quite possible that the autistic behavior was a side effect of those, rather than her actually having autism.
Bit of a disadvantage since I haven't actually read the book and don't really know exactly how she was written, but the the impression I've gotten is that the author basically shrugs the whole thing off as if it was "just a phase" rather than a lifelong emotional condition and is now completely "normal." I suspect that the writer either knew he didn't have the chops to portray autistic behaviour or was just lazy and couldn't be bothered to deal with it. From what I've read about the guy, either option (or both) are equally likely.
The way I see it, however much she may have opened up and improved over the last two or three years since 'Ascension', there's no way there wouldn't have left it's mark on how she thinks and behaves. That plus the impression I had was that Cerberus's medication had compounded an already existing condition, not created it. Even if it had, autism is a neural development disorder that has a very real physical effect on the way a person's neurons connect. Their brains are literally wired differently. While it's true that there are varying degrees of autism and some are functional enough that they can take care of themselves and pass for "normal" (for lack of a better term), whichever way you slice it, Gillian's condition was pretty damn severe--at times bordering on catatonic--for almost the entirety of her childhood. Drug induced or not that MUST have a noticeable impact.