OK, if that's the case and she has no power over her songs composed with SC to ban others from using them, we can assume the fans calling for her to ban Kalafina from using her music were uninformed but just eager to have Kajiura take action against the slight on her role as the creator of the group. They assumed she had the kind of power to challenge their taking her name off the promotion of the concert.
The question is, if she actually had the power to ban them, would SC have insisted on her name being stripped from their reunion plans? They would have been wary of her ability to play that game with them. Another question, is would she? Probably,
if she could, I suspect she would.
So Kajiura's hands were basically tied.
I wonder if that came up in conversation during the planning stage of the reunion concert, that Kajiura couldn't prevent them from using the music. The question I have is, ""
why keep it secret from her if she couldn't stop it from happening?
" (assuming @Westkana is 100% correct).
If they included her name, would SC have had to pay her more? I don't think so.
If they wanted to use her name SC would have to get her permission, so they just decided to bypass all that by not having any contact with her in any way, and getting the girls to do the same. Or did SC approach her earlier and she said no, so they decided to remove her name from everything, and get the girls to follow suit?
If she couldn't stop it from happening, why did the ladies agree to keep it from her? What could she have done? 

If Keiko and Hikaru met with her and asked her that they wanted to reunite with Wakana and do Kalafina could she have convinced them not to do it? I doubt it.
Kalafina fans (though I am one of them) who are less fond of Kajiura (I am not one of those) have continued to have the impression that the ladies were all innocent bystanders in all this, or they were forced, and should face no backlash or "consequences", but that's just (1.) naive and (2.) incorrect.
They made and committed to
decisions and chose who, and how, to associate with and
not associate with. They couldn't hope to control anyone else's reaction/response (fans or Kajiura) irrespective of any feelings or expectations they had about their decisions and those reactions.