As I am sure you are aware Exchange can handle multiple mail domains and you can set each users default mail address within Active Directory Users and Computers. You can set the exchange servers to talk to and through each other if you want to keep both exchange servers. With domain B having so few users it must be fairly easy to migrate them to domain A and maybe integrate the server as a member server with/without exchange as part of domain A. This looks to be pretty much the way you were thinking anyway,
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