A commitment to privacy and principles.

Fundamentally there was no viable way to get permission from the freenode user base for that in a way that was morally acceptable.

(I'm sure there were legal reasons too but I don't believe the question ever got as far as that being relevant)

What good would that do, if the users aren't connecting to the network?

> What good would that do,

It would save both staff and users a lot of time from having to re-register accounts, channels, and projects/communities.

> if the users aren't connecting to the network?

I don't understand this part, sorry.

If your users are on Freenode and don't know about your network, having the structure there doesn't do much good. It doesn't take much time to register nicknames/channels anyway, certainly not enough to risk a lawsuit from Freenode.