There are stories that Musk was willing to foot the bill. Of course thats easy to say after the other decisions have been made, but my guess is my second point was probably the real no—at least not in a timely or safe enough manner to make the overall future mission disruptions worth it from NASA’s POV.
It also forced NASA to completely change their safety standards. In particular NASA requires there be a 'lifeboat' on on the ISS for all crew in case of an emergency, but because of the Boeing crew (and the lack of a corresponding vessel), NASA approved a new 'configuration' of the Dragon where up to 3 people could strap themselves to the floor of it, where cargo would normally go, in case of the need of a mass escape from the ISS. [2]
[1] - https://en.wikipedia.org/wiki/SpaceX_Crew-9
[2] - https://en.wikipedia.org/wiki/Boeing_Crew_Flight_Test#Uncrew...