It was not who is right but what is right,we all think,that

matter在这里是不及物动词 （vi.）可以理解为：要紧,有关系,所以不用were.句子中间的we all think 是插入语,句子主体是强调句：It was not who is right but what is right that matters.
matter 例句:
It does not matter at all.
毫无关系.
It doesn't matter throwing that away.
把它扔掉,没关系.
It never mattered what time of day or night it was.
不论是白天还是晚上,都没有关系.
It doesn't matter much whether we go together or separately.
我们一起去还是分头去都可以.
再问： 如果去掉强调句型 it is ....that..恢复句子是Not who is right but what is right matters对么？
再答： 是的，不过一般不这么说，只是语法上可以这么分析。一般就用强调句式表达类似的意思