I will share criteria that I use in order to determine whether someone's writings are intellectually honest or not.

Firstly, intellectual honesty does NOT mean neutrality. It is perfectly possible to have a preferred position on a subject (it can be in the scientific minority or not, that doesn't matter) without being intellectually dishonest.

Here are the criteria.

1)Transparency. Do they hide that they have an agenda/preference or is it public knowledge? Do they hide behind scientific neutrality or do they openly admit that they are interpreting facts according to a philosophical/religious position?

2)The use of sophistry in their writings. Are their writings logically sound? 

3)Are the categories they use clear? Is the language understandable or is it purposefully obscure?

4)Do they accurately represent the scientific opposition and answer to the real counter-arguments from the scientific opposition or do they tend to strawman their opposition?

5)Do they use force or threats in order to neutralize scientific opposition?

6)Is there a double-standards for what constitutes evidence? As an example requiring irrefutable proof for opposing positions but using shaky proof for their own position.