This is what is known as "neglecting context". Right after the sentence you originally quoted from the article, we see this:

They must recognize "faith" as an attempt to disconnect their beliefs from the voice of the evidence; they must vow to protect the ephemeral correspondence between the real world and their map of it.

I'm not quite sure why you're having difficulty understanding this. "Willing reality into a being a certain way", in this context, does not mean desiring to change the world, but rather shifting one's probability estimates toward one's desired conclusion. For example, I have a strong preference that UFAI not be created. However, it would be a mistake for me to then assign a 0.00001% probability to the creation of UFAI purely because I don't want it to be created; the true probability is going to be higher than that. I might work harder to stop the creation of UFAI, which is what you mean by "willing reality", but that is clearly not the meaning the article is using.