I really think we're underplaying the long-term consequences that going public will have for Negi and the gang.
Don't know why everyone feels this was rushed either. We all knew from the moment this mission started that it would end the moment they got Asuna and the key. They set this up quite nicely so that this final mission was really less the end of the previous arc and more the beginning of the upcoming one.
Think of it this way. Pretend like the arc ended the moment Negi unraveled the mysteries of the world and this has all been the beginning of his journey to save the world from its' inevitable fate. Goes through some inner turmoil, comes up with his plan. Step one is dissuade the people who are using other means to deal with this, rescue his friend, and recruit some help along the way. Now that he's gotten that out of the way he can get down to business with the whole preventing the apocalypse thing.
Really ever since that revelation there have been bigger concerns than the return of Ala Rubra's old foes. It's part of the continuing coming of age story that is Negi separating himself from his father. Nagi was just concerned with the immediate threat of the alleged bad guys. Negi's actually concerned with the same problem as the villains, but sets about coming up with a more productive solution. Whereas Nagi's goal was to take out the baddies, Negi has the same goal as the villains with disagreement in methodology that needs to be overcome.
These guys were the final boss for Nagi, but they were never so for Negi. For Negi these are allies in the making or competition at the worst, but ultimately a much smaller concern. Negi's a big picture kind of guy. In many ways he's already surpassed his father.