So your saying instead of being considered one model as a mountrous beast would you would have each sister be targetable, each have 3 wounds (total 6) and on the off chance they are each killing blowed in the same phase/turn the eagle then gets to react but otherwise wouldn't?
Interesting. I kind of see the logic, seems fine to me other than the reaction really. To me I feel the Eagle they ride although has the same stats should be considered a monster. Therefore you would play them as you would a dragon rider. The bad side to this is it is not a monster so I am just saying it is. Very messy.
If you keep it as a monsterous beast then you effectivly lose 4 wounds as you would only use the highest wound set meaning 3 and they would all be considered a single model meaning as you pointed out they could be killing blowed which would kill them both (all 3 counting eagle) in 1 amazing attack. The eagle would regain its wounds backto full if not killed though as per the rules for the sisters even though its really the eagle healing. So damn messy.
First instance you are just saying the eagle is a monster not a monstrous beast, people will complain as you would then get thunderstomp.
Second instance You are losing 4 wounds of the sisters, 1T of the eagle, monster reaction if the sisters die and the sisters being able to skirmish if the eagle dies.
I know what your opponent would want you to use. I'd be quite happy using the second one myself if it weren't for the FAQ saying about the monster reaction. I just don't get how it would work since the eagle dies when its (3) wounds are taken (killing blow or any other way.