I've seen you do it.
It's possible that you genuinely don't believe you do, but everything you have said thus far is a pattern that has played out pretty much any progressive idea has been presented in mainstream media.
"I'm not homophobic..." Or racist, or sexist, or transphobic, it changes depending on whatever the particular progressive idea being presented is. "...but..." because the previous sentence is always an effort to try to appear reasoned before going into the actual argument "...I don't know, I just don't feel this is natural. It's like they're pushing an agenda." And then you become hypercritical, trying to magnify minute or even imagined errors into something way bigger than it actually is, a standard that isn't really applied in otherwise typical critical analysis. It's all pretty rote.
I'd like to address the agenda thing in particular. Assuming you're being disingenous, it's just code. The false argument being presented here is that somehow a straight romance is agenda-less. The truth is, any form of narrative is a series of decisions made by a person, and the purpose of a narrative is to provoke some kind of reaction. The agenda of Harry Potter is to capitalize on people's desire to enter into a magical version of school. The agenda of Uncharted' Elena is to play on presumed male audience's desire to enter into a romance with a hot blonde woman. There's more to it than that, of course, but there is no narrative without an author trying to actually DO something that makes you react some way, and straight romances do that as well.
But no one ever goes "That author had such an agenda trying to push that Elena-Drake romance on me." Even if people don't like the romance or find it unbelievable or bad (twilight or 50 shades being easy targets that come to mind), nobody ever puts the criticism of the author having an agenda because of course they fucking did, they're storytellers. The agenda is to play on people's desires of seeing a romance come into fruition. But when, for instance, the subject matter is something like gay people, agenda's come up as if they are not the part and parcel of the concept of having something to say in a story. As if stories were real and not fictional, man made things that have real people making deliberate decisions of that universe. So yes, Ellie and Dina kissing is agenda driven. The agenda is playing to people's desire to see a relationship blossom to fruition, which is functionally identical to hundreds of thousands of stories before it, except this one's gay.
But lets give you the benefit of the doubt. Lets assume you're genuine and what you say are your best attempts to articulate how you actually feel. Assuming that is true, you're still giving off a homophobic vibe, just one in which you aren't willing to cop to the idea that you are in some way uncomfortable with the depiction. In a way, it's not unnatural that you would be. Part of benefit of experiencing new types of stories is that you see things that are truly new, if only in a slight way. For example, remember back in the second trailer, we had a thread where people discussed how they were uncomfortable with how the trailer showed the characters brutally killing the woman who was about to kill the new cast of characters? If that character had been male, that conversation wouldn't have happened because we are used to dehumanized male enemies, it's....kinda wierd seeing female enemies being treated with that kind of brutality and being so casual about it. It's only a slight change, a female evil bastard instead of a male, but it's genuinely new, or at least as far as mainstream stuff goes, and that means we process it differently, and that process can be sometimes uncomfortable. In that way, I wouldn't wholly blame you for being slightly uncomfortable at seeing a gay couple kissing, especially since it's being framed as not for male titillation as so much lesbianism is (and why it's more readily accepted than male gayness), but for gay women.
That's just gonna feel weird at first to most people, whether they're deliberate homophobes or not. And that's okay. We've lived our entire lives in a culture that has pushed more the more malicious agenda that being gay is a sickness for a very long time. It's gonna take a while before we work everything of that out through our cultural system. Progressive storytelling is to work to that purpose. It's goal is to make the idea of a gay relationship normal. There is always going to be an agenda to gay relationships in storytelling, but maybe in the future that agenda will be as invisible to people as the agenda behind straight relationships is now. But until we get there, we have to be honest to ourselves. It's not, and that's means it's gonna be new, and we all need adjustment to new things.
Of course, this is all my own conjecture. I'm not accusing you of anything or even telling you you necessarily did anything wrong. I just think this "It's about ethics in games journalism the art" line you've got going is horseshit. Intentionally, unintentionally, who knows, but it plays into the exact pattern I've seen a thousand times at this point.