I really don't know much about the disease, but I don't think that JRD is directly causing her aggression. Dogs can display aggression when they aren't feeling well, which is more than likely what is going on with Millie. Her condition might cause her to not feel well, which in turn might increase aggressive behavior, but I don't think that it is specific to JRD. She's also in the "teenage" stage right now, which is known for causing kooky behavior in even the healthiest pups

I know many members here have posted about their boxers becoming more guarded, more fearful, and even more aggressive towards strangers as they go through the teenage phase... mine included

She's 2.5 yrs old now and has gotten much, MUCH better about it.
How does she react when she sees a strange dog? And what are you doing to calm her? It's also possible that the methods you're using currently just aren't working for her. Not meaning to criticize, just wanted to throw that out there

Maybe a different approach to training is all that she really needs.