Did Alice really love Tom before she laid eyes on Lukrasta? She kissed Tom before attempting to read the 'Doomdryte' and there has to be strong affection if she kissed him. Also, are Lukrasta and Alice really 'soulmates'? Do Alice and Lukrasta really truly love each other?
You will have to wait for the next book, The Dark Army, when all will be revealed. We will find out why Alice did what she did.