The powerful barrier Azurea had spent so much effort reinforcing—the only thing keeping the sea monster trapped.
If Naya's promotion went unchecked, the sheer elemental disturbance could disrupt the seal completely. The very thing she had been fighting to prevent.
Even worse was the fact that she couldn't get rid of Naya at this point. Unless the ascension ceremony failed and claimed the aspirant's life, nobody else was supposed to interfere in it.
Firstly, that would make her spend more of her efforts– efforts she could use to complete the barrier strengthening process. She literally and figuratively had her hands full dealing with the mess that Eren had brought along with him. She had already messed up the ritual a little by taking her time to deal with the Templars.
Anymore mistakes, and her side of the seal would just crumble apart. If and when that happens, it wouldn't take long for the mana barrier to collapse from Shir's side as well.