First of all, how do know what took place in negotiations? You don't. So, it's not that "obvious". It may have been negotiated for, or it may have come as a recommendation after he was hired, which is more likely. Otherwise, there wouldn't be this uncertainty on whether the hire will be allowed. If it was a demand by Freeman and agreed upon during negotiations, then the whole "package deal' would be in question.
Second of all, what is wrong with a coordinator wanting his support assistant to be hired along with himself? Even is it came as a stipulation of his own hire. A person can ask for whatever he wants during negotiations. I seriously doubt that he held a gun to the heads of Kelly and Swarbrick. They were free to say no if they felt it was inappropriate or unworkable. I, for one, like that ND is thinking somewhat out of the box regarding their recruiting efforts.
Bad optics? Meh. To whom does it look bad. If they can lift the hiring ban, they will, and not many will really care.
As far as the NCAA looking into putting limits on analysts and support staff, that's a different argument. I would NOT say you're wrong on this. I haven't looked at the size of other schools' support staff. Although, I'm sure there are many that have larger staffs than Notre Dame. But, it's not very transparent, so I haven't seen hard numbers and don't have a strong opinion on the matter. I would say it's worth looking into by the NCAA, but I think the NCAA is more likely to lose their jurisdiction over college football before too long. There soon might be a new structure for governing football.