Yes, your summary line at the top feels like exactly the distinction I was trying to make. Rereading my comment, I think I was attacking the straw man position, that after admitting that EY had said rationality and feelings were not orthogonal, I was arguing as though he'd said they were the opposite of that - directly related, parallel, etc.

You could explain Eliezer's non-standard approach in terms of his being fundamentally different to many in that regard; or you could explain it as depending more heavily on his situation: he was a highly intelligent atheist surrounded by confused religionists. Alleviating the confusion from your pain is surely a thing one would hold up as in that situation.

"A distinction should be made between seeking comfort and seeking comfort in false beliefs. The former is acceptable and the latter is unacceptable."

A fine quote.