Autistic parent of autistic kids here.
She likely wants to stay at the grammar because it's familiar. Change is difficult for autistic people and the last two years have brought huge changes. My DD is in year 12 and she's really struggled with lockdowns, the gcse process being so confusing and transition to sixth form. She's only just settling now and she's got one to one support currently and still sees most of her school friends and is in a couple of classes with her best friend.
Your goddaughter also has pregnancy to contend with and as an autistic parent I found it incredibly difficult. It's a sensory nightmare, everything is unpredictable, everything feels overwhelming.
She is likely clinging to school as a constant in the sea of unpredictable chaos. She won't have thought about how repeating means she won't be with her friends any more. She also won't be aware of how horrific and none existent the SENsupport is because she doesn't know any different.
I suggest researching all the options. Find out what school can offer then find out what other options there are. I'd advise having all the information then going through the reality of each option with her. Once the baby is here she may also change her mind so prepare for that and try to avoid having to make a final choice until after she's had the baby and found her feet a little.
Also consider that SENsupport makes a huge difference. We had things like the leave lesson card in place for my DD even before diagnosis. They made a huge difference.
A levels are much more difficult and require a lot of independent study and organization which is often a weak point for autistic teens especially. She will need support. As much as you can offer.
Don't reject anything, stay open minded, work out the options and go from there. Make sure that your Goddaughter also has an understanding of her options and decide together. She should be guided and supported but IMO it's her choice.