Pak, this is ridiculously much like what I am facing right now, just with less time travel involved! We just moved much closer to one town than we ever were to the other town DS is at school in, and this is throwing out some kinder decisions, as well as DS' schooling for next year (sucking it up at current school for this year and possibly next year or the next 5 years! Limbo is not the fun it's cracked up to be).
In your case, it sounds like your last option would be the easiest to deal with as a family. Once she moves to school A then you will ALL be in a new area and making new friends, not just DD, and you will on that adventure together. Once you've moved to the final school, chances are she'll stay there till the end and have lots of time to develop security there.
Just my thinking, but if you don't have to be a long drive from school, then don't be, for the reasons you've outlined. Spending that much time in the car will affect everyone. A bus trip after a drop off locally is a different thing and country kids get used to it to get to a good school (and for some, ANY school!), but they're in it together and it's the bus driver's job. 45 mins one way is a LONG time you could be spending on other things, and money you could use on something other than fuel.
Just food for thought. I most definitely feel for you and wish there was a ready made answer. xx