My issues with the episode was not this (more of she gets her Pinkie Sense seemingly out of no where, and is never referenced again until Mare-Do-Well), but think this isn't the issue, or at least, not in its full complexity.
I am fine with other people having different beliefs. As long as they don't try to justify being a jerk because of those beliefs, I really don't mind.
The issue here is more that it seemed to suggest that you had to accept things that you could not explain, and you shouldn't bother to try to explain it. I don't think it meant to come across like this, and I think people are over analyzing it.

My problem with this episode is not how Pinkie acted but how Twilight acted. The episode completely destroyed anything that could be called the scientific method. Sure, Twilight was critical of the ability, which is good. Critical thinking is a feat. But her research went on to be bias and all she wanted was to prove the pinkie sence wrong, ignoring all the evidence to the contrary. There was a clear correlation between Pinkies behavior and the things that happend in the imidiate future, she had to acknowledge this. She did at the end, but in the wrong way. She gave up; which makes science look like something you can simply replace with belief. When we're on the topic of “faith” I see no reason why it had to be address it in the first place. You don’t need faith to see that something is going on, you have evidence.