Ok, so picking out what you have said:
She had complex surgeries as a newborn and as a child
She has medical needs
She has an EHCP
She has an occupational therapist
At least two referrals have been made (? for ASD) but have been rejected due to "mixed profile" which I would guess probably means that that the ASD assessment people are of the opinion that at least some of the behaviours are due to her medical condition.
She has a 1:1 at her primary school.
She can't write more than a few words and uses a computer to type.
The primary school are worried that Mainstream secondary is not the right place for her.
The picture I see here is a severely disabled child with complex needs. Clearly she is diagnosed with at least one possibly more diagnoses, and with an EHCP in place she is getting (some of) the support she needs in education.
I'd suggest getting in touch with the charity for her medical condition and finding out how it is likely to change as she gets older and what support is best for her. They may well have advice on which (eg) sporting activities will help develop her body and which are likely to be too much for her.
In terms of schooling, there are advantages and disadvantages to both special and mainstream. With an EHCP you should be getting annual review meetings and it is worth talking to your school about what secondaries there are locally and how they would cope with her needs.