The dog barked because he or she was shut away in a room in an unfamiliar place, and smelled a cat.
The cat was nervous because of 1) strangers in the house, 2) a dog barking, and 3) that dog was in the house.
They were ungracious guests, the dog was unhappy, your cat was unhappy and you apparently were unhappy.
Of all the parties involved, the dog appears to have had the least say in the matter, followed closely by your cat. It may have been worth the upheaval in your home, to aid in the setting up of this nonprofit. Or, maybe it was not. Sounds as if you would have done things differently, in hindsight.