what 在主语从句中,代替的是：her family.
你举的那个例子：i wonder what your name is 并不是主语从句,是宾语从句,what从句 在句中并没有代替主语,而是宾语.
what was most important to her,she told me,was her family
首先,把插入语,即she told me去掉
然后,明确,主语从句中what 在主语从句中,代替的是：her family.
句子变为her family was most important to her
所以,仍是陈述语句,不矛盾.