I'm married to someone who thought I was a man (because I thought that, too) , so although she is bisexual, there was still a significant bait and switch going on. Much like your guy, her orientation included my target gender, but she was used to the penis...
Anyway, it's generally a reassuring story, if that helps.
Yes, the recovery process was no fun, and we both were pretty stressed out and miserable for the first week or so. But that's not unusual for major surgery, even when the genitalia aren't involved. Once I was more or less up and about it got easier, and so I do literally mean the first week to ten days were tough. We did have to wait for sex for a few weeks, but that wasn't too hard. She says that she never had any real problem differentiating between "surgical site" [not sexy at all] and "functional vulva" [good for sexytimes] once everything healed up, and that by a few months later she'd mostly forgotten the bad bits - pun intended. These days she occasionally notes that my parts are prettier than hers, and otherwise has no problem enjoying them.
It seems as though you have to believe your guy when he says he's fine with you doing this, if only because second-guessing him is probably more harmful to the relationship than surgery. As for the actual physical healing part of it, if you're really worried you could try to keep from showing him too much gory surgical aftercare, but that part is fairly brief.
(2 years after my GRS, my wife had an ugly abscess on her breast that needed surgery. I helped her change bandages etc. and went through some of what she did with me, including the lack of sex until she healed up, and I also still find her sexy.
The lesson being that marriage sometimes does literally involve taking care of someone when their body misbehaves, and there's no guarantee for you *or* him that neither of you will ever end up needing surgery. At least this one you can prepare for, and you'll be filled with happiness afterward.)
