I think one of the reasons that people take Alina as The Big Bad is that they want to latch onto a villain and she is the first visible one. I think mentioning her in just the right place and time might help people get over that. Maybe getting a prominent agreement to the that effect, perhaps repeating the discussion with Katerin and without her could help maintain context.
A protest by Kha in the 'I challenge you' meeting to the effect of 'this is bigger than you, you petty cow!' might also help, especially if Alina brushes it off.
The pacing of the main story is also a problem. There are just too many long stages. I realize you have clews buried in some of them, but you have nine unrelieved chapters. If, by one of Sil's runes, you could get it below six chapters the difference would be huge.