Nor, if regularity and conformity to a standard pattern are as desirable to the scientist as the writing of his papers would appear to reflect, is management to be blamed for discriminating against the "odd balls" among researchers in favor of more conventional thinkers who work well with the team. 

你的理解基本正确。第一个as是副词，第二个as引导比较状语从句，as在从句中作reflect的宾语。因此as是个关系代词。其实as引导所有的比较状语从句时都是要在从句中作成分的，它不是从属连词，这一点和than是一样的。不必将从句看作定语从句。就是一个比较壮语从句。

if条件句翻译如下：

如果标准模型的规律性和一致性就像该科学家的论文中所显示的那样理想的话，……