I can see why one might be apprehensive to rely on the trustworthiness of reasoning. I'd say if one wants to keep their sanity, the easiest way would be to continue to rely on reasoning. After all, if one throws out all reasoning then one's thoughts would seem to be rather meaningless since there would be no reason for them.
You may say that under my worldview all thoughts are meaningless anyway since they're merely based on physical responses and/or signals within a brain. To that I'd respond that mankind assigns its own meanings to these mere physical responses or signals.
I will assume that you haven't abandoned all reasoning since you're responses are an attempted form of reasoning.
I don't think that humans can be sure that their reasoning isn't completely or partially flawed. This would apply even if there wasn't a solely physical form of thoughts. Under your world view, you "believe that reasoning and consciousness supersede mere chemical and material explanations". Does this point to reasoning through these processes being more reliable or true? I would say no it does not.
Without proof that there is other thought processes beyond the physical realm, I'd say one can't say decisively the reliability of such forms of thoughts. We can't examine them at all.
You might think that reasoning is a gift from God. How did you arrive at this conclusion if not through the (possibly flawed) act of reasoning? It could be Satan influencing you into incorrect thoughts about reasoning.
To sum up, I'd say no matter the worldview, one can't 100% say that reasoning is reliable. It's probably in our advantage to assume that it's at least some what reliable as the other option is throwing out all reasoning/rationality.