Could be that.
I think Freeman has a few things going for him.
Kelly did not get off on the right foot when he got to ND and I can imagine the BoT and other admin were hesitant to put their faith and assets into his program. Keep in mind, the first two seasons, ND went 16-10 and we had to endure the Declan Sullivan tragedy as well as the Lizzy Seeberg all in the span of 2 years. Then, the second ND finally sees some legitimate success under Kelly, what does he do? Interviews for another job. How could the university put their faith in him at that point?
Freeman is just flat out far more likable, charismatic and I think he has a clear vision for ND that Kelly never really seemed to have. He would coach-speak his way around it, but with Freeman, you can tell he's being genuine and isn't leaving the fanbase in the dark. He knows what needs to be done and I'm pretty sure he's going to be persistent that ND does what's necessary to make sure he and his staff are best equipped to compete in this new CFB landscape.