I would like to argue that there could be a more tolerant view of religion/theism here on Less Wrong. The extent to which theism is vilified here seems disproportionate to me.

It depends on the specific scenario how terrible religion is. It is easy to look at the very worst examples of religion and conclude that religion can be irrational in a terribly wrong way. However, religion can also be nearly rational. Considering that any way we view the world is an illusion to some extent. Indeed the whole point of this site is to learn ways to shed more of our illusions, not that we have no illusions.

There are the religious beliefs that contradict empirical observation and those that are independent of it...

A) Could it be rational for a person to hold beliefs that are independent of empirical observation if (a) the person concedes that they are irrational not empirically based and (b) is willing to drop them if they prove to not be useful?

B) Could it be rational for a person to hold unusual beliefs as a result of contradicting empirical observations?

As a least convenient world exercise, what is the most rational belief in God that you can think of?