Waters and Jones leaving at roughly the same time suggests to me that the RFU, rather than Borthwick, are the main reason for the departures. Maybe it was a matter of finances or T&Cs not being honoured, but Waters and SB were together at Leicester so each one knew the other on a daily basis and Waters would have given Jones a fairly deep insight into SB's working practices. To me it looked like SB was giving his coaches a free rein after the Scotland 6N game and this appeared to carry on over the NZ tour.
They'll both be sorely missed as I really had hope for the next RWC cycle, but it surprised me to learn that Tom Tomblson had already left (apologies if this has already been raised elsewhere). Can't help feeling that this isn't down to Borthwick.