RC - well, I can answer some questions! I'm not sure if vaccine exemptions owing to health or religious reasons are accepted at schools. However, I would suggest calling Abu Dhabi Education Council and asking this, as the rules will be the same for all schools. Schools, at the the behest of HAAD (Health Authority Abu Dhabi), do run vaccination programmes during the school day. I have always been contacted ahead of time, and given the option for my child not to participate. I am not anti vaccinations per se, but I like to avoid unnecessary vaccinations / exposure to chemicals where possible. Last year my daughter was exempted from the additional MMR vaccination at my request.
I am absolutely not criticising your choices, as I understand entirely where you are coming from, but just want to flag to you that the herd immunity that may be relied on in other countries is not present here, as there is a large labour force from India, Pakistan, Bangladesh, etc, and measles and other sicknesses are not unknown.
There is a large home schooling group in Abu Dhabi. I don't have contact details, but an internet search should get you started off. I hope this helps!