不是的.
whether she will join us 这是个主语从句,表达是未来的事情,故用了一般将来时； 而 won‘t make 是主句的谓语动词,刚好表达的也是将来的事情.它们互不冲突.
但不是说,凡是前面用了will,后面也一定得用will或won't.具体要看表达的需要.如：Whether she will come to our party isn't unkown./ Whether Liu Xiang will win the medial in the 2012 Olympics has been great conern among people.
其实楼主的句子,主句也可以用一般现在时,而表达的意思与原句没多大区别.即Whether she will join us doesn't make too much difference.

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