You know, thinking of Chisame's situation, Perhaps she become something of the Oracle to Negi's batman.
She may work from home, but she's effectively telecommuting, as well as using the sprites and such to gather information and dispense the necessary advice.
The only reason I can think why she's not doing all this in person is with Asuna there, she doesn't need to be by his side to keep him from doing stupid crap. In the alternate timeline, I get the impression that's one of the roles she settled into.
So basically, Asuna's return screwed her form that perspective.