Well - I'm not a StructureMap dude myself, and I must admit that I've never tried to make Rebus work with nested containers/child containers.
But I would think that you could make it work if you implement a handler activator and a unit of work manager yourself, which you can enable like this:
Configure.With(yourHandlerActivator)
.Events(e => e.AddUnitOfWorkManager(yourUnitOfWorkManager)
.(...)
and then you can use that unit of work manager to create a child container that you stash in the message context like this:
MessageContext.GetCurrent().Items["some-key"] = yourChildContainer;
which you then fetch & use in your handler activator when the time comes to resolve the handlers.
The child container can then be disposed when the unit of work is over, thus releasing stuff properly.