Dean was totally content with keeping his and Cas' relationship to themselves. He was fully prepared to indefinitely leave Sam in the dark about the whole thing.
But when Cas mentioned the possibility of Sam walking in on them full-frontal (a scene that was becoming more and more likely), Dean was forced to reconsider. He'd been admittedly disappointed when they'd told him, Cas using words like "intimate" and "romantic," making Dean blush, and Sam had simply started laughing before he confirmed that he had already known.
Turns out you can only stave off suspicion for so long after so much whispering behind closed doors and waking up to suggestive noises. And it turns out Dean can only take so much of that conversation before he needs to get out of the house and take a drive.
As far as everything angelic goes, their heavenly problems seemed to end when Naomi did. Castiel had grieved for a while about his family that had died in order for him to be rescued and for him to make his escape, and Dean had a feeling that when he said he was over it he was just putting on a brave face – something he'd probably learned firsthand from being around the Winchesters for so long.
Dean couldn't really call him on it; he was busy doing the same thing. He knew he should be happy, should be ecstatic that they were both alive and it seemed like they would be for a while at least. But not being able to sleep with Cas, not really being able to feel Cas, not being able to grow old with Cas – it weighed on his conscience all the time. Luckily, Dean Winchester had always been the king of emotional suppression and he kept his mouth shut about his minor (and one major) concerns.
So when Cas left the bunker for the day without offering an explanation like he normally does, Dean was curious but he didn't question it. However, he had plenty of questions when Cas returned with another person. Another angel. Turns out Castiel wasn't as unobservant as Dean had suspected.
Cas' grace transplant had taken a lot from him, but he managed to maintain his subscription to angel radio somehow, something he had failed to mention to Dean. It had taken time, but Cas had tracked down one of the few friends he still had on his side up in heaven and when he heard he was going to make a quick trip to Earth, Cas was sure to be there to meet him.
"Surprise," Cas had offered when Dean had started in on his first questions concerning the random angel's presence. Instead of explaining he'd simply asked, "Are you ready to be human again?"
Dean wasn't stupid, he could recognize the merits and advantages of having someone with angelic powers in their midst, the Winchesters could always make use of a good healing, but he had a lot of trouble focusing in on those facts when Castiel dangled the choice in front of him.
"How's it work?" had been Dean's eager response.
The de-gracing had been (minimally) painful, but it went off without a hitch. It tends to go a lot smoother when you don't have to literally rip it out of yourself with your bare hands.
Cas politely declined taking it back in himself, the thought of permanent humanity and free will proving to be too enticing. It wouldn't have really solved their mortal-immortal dilemma, either. Dean guessed he was still more than a little traumatized from what he was almost forced to do the last time he had it in him. Plus it's not like it's permanent. Now the grace just sits in a sort of locket around Dean's neck, where it's well protected according to Cas. It's always an option in case things get too desperate.
Dean's pretty excited about the whole 'having-a-soul-again' thing and not having to cease to exist if an angel blade finds its way into his heart. Now there's the promise of an afterlife. And as funny as the word "forever" sounds coming out of Cas' mouth, Dean's pretty okay with the idea.