First of all, they did not attack first. They were in Pakistan helping the Afghan Taliban across the border by providing refuge, attacking NATO supply lines and so forth. The Pak government then attacked them and they defended themselves, whilst also making (legitimate) takfir of them. Not only this, but since the government of Pakistan has shown its open hostility to Islam and they are clear apostates, then it is permissible to rebel against them just as it is permissible to rebel against Bashar al Assad in Syria. What is the difference between them?
And bayah cannot be given to a kafir, it can only be given to a Muslim. The bayah they have given to Ameer Ul Mumineen is to show they accept him as their Amir in the war and that when they win, they consider him to be their legitimate leader

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