The author is merely saying that he personally sees a use for religion in seeking comfort from the reality of death and suffering. And that (to a group that shares a similar world view and set of beliefs) it is okay to stay within that world view to seek meaning and comfort in these situations. In addition, the author points out that he has difficulties with certain beliefs but sees usefulness in the "opiate of religion" (for him personally) when it comes to grieving and facing these situations. People choose to grieve as they see fit. If the author states that he "believes in God and prayer" we don't know much of what that means in this article since it is besides the point.
The author has to assume that the preacher literally believes in what he is preaching otherwise the preacher would be in the wrong place and being dishonest. And assuming that the preacher literally believes in what he himself is preaching, what the preacher prescribes in this situation is the appropriate prescriptions for the people who follow his world view.
For example, if I were to go to the funeral for this 17-year-old, it would be wrong and out of line for me (in my personal opinion) to be honest about my own views on what happens after death since it goes totally against the grieving family's world view. In other words, honesty is not always a virtue in my opinion. Expressing how ugly someone truly is or looks or making someone feel bad because he/she interrupted me with the "I am making you feel bad for the sake of honesty" justification are not virtues in my personal opinion. I see honesty in this case as justification to hurt other people and I see that as harmful.
And I don't think the author was trying to say he was more enlightened than the people attending the funeral and I can see he was just assuming that everyone attending the funeral believed literally in what the preacher was prescribing since he said that he doubts "that a single person in that chapel doubted for even an instant that every word that preacher said was literal fact." But again, he is stating this in support to his main point (that the opiate is perhaps the best prescription for people holding this world view and that the opiate may be useful to himself for self help) and not that he was more enlightened and (even less) that he was trying to be rude by seeing these people as inferior in any way.
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