Rather than "merge the designs", as a way to pick the better of the two, you could suggest a blind test — get a few neutral people whose opinions you both respect (you say its for a parish, there should be plenty around who have an interest in the outcome) to look at the designs and offer their input as to which is the better one. That way it takes the personal out of the criticism if that’s what you’re worried about.
(If/when his design loses, perhaps you could find an aspect of the parish where a micro site with a different look and feel would make sense and let him start over with reign of that part of it, and you do the main site)
Honestly though, if he wants to be a designer on a professional level, he needs to learn that critique of his design does not mean "putting him down". You aren’t helping him in the long run either by pacifying him in order to be polite. The critique needs to be honest and helpful, of course, and needs to include the WHY you don’t like it and how it could be improved, but a huge part of being a designer is hearing "I don’t like this (or) this just isn’t working — please try something else." — and not taking it personally.