@LordVincent is definitely right about this. It's the intent behind the story. If this is someone who's trying to hurt someone and just happens to be gay, that's ok. Anyone is capable of hurting someone.
But if you're saying "BECAUSE they're gay, they're doing this", then it becomes a problem.
It's also good will to have a warning up for your work. If you know you're dealing with darker themes, it's still good to warn viewers that these themes will be in there. But when it comes to staying within the guidelines and not getting a strike, you have to ask yourself this:
"Is there a way for me to show this in another way? Do I REALLY need to show this in a detailed way?"
For a war torn scene, there are different ways for you to show and imply actions without explicit details. Take a look at this page from the last arc of Bleach:
This counts as a war torn scene. You can tell people have been murdered, but it's done discretely. You don't need a lot of harsh details to know. We're also given a view of character reactions, which I feel help highlight more to these scenes. After all, you'll leave your readers to make up the image for themselves, to wonder "just how bad was it?"