Theory: Part of the reason the final scene plays out the way it did is because the player picked the wrong combination of party characters. Though Iron Bull is powerful, Sera wasn't a good support. Back when ME2 first came out, there was the whole "Mordin glitch" fiasco where people kept having him hold the line and he kept dying. Then finally everyone realized, he was just a bad choice for that part of the mission and it wasn't a glitch.
I've always wondered why everyone kept saying "don't have Mordin hold the line" at the end. Never had any problem with that, personally. If you save everyone else, and make sure you leave enough party members with him who can hold their own, he'll be fine.
My point is that it's a decision that actually makes sense. He's a weaker character, and he would not be able to handle his own in a situation like that, without enough backup. But most importantly, you are aware of the dangers when making the choice.
If this mission is designed so that whoever you bring with you has a possibility of dying at that particular moment, then there would need to be a serious warning prior to beginning the mission. Because everything we saw was an outcome to a decision we never even saw the Inquisitor make, (sending Leliana on that mission) and never once did the Inquisitor make a choice that affected anything in that confrontation.
From everything we've seen, my money's on her being knocked out. My guess is that they cut right before either Leliana is killed (because we know this is the outcome of sending her on this mission, and her getting captured), or right before the Inquisitor makes a critical decision. That decision may influence whether or not Sera/Iron Bull die - but I think it's more likely to influence whether or not Leliana does.
Again, this is purely speculation based on what we saw. However, I find this scenario *far* more likely than Bioware unceremoniously killing off 2 party members off screen, based on a choice made prior to even starting the mission. I mean, these aren't Skyrim party members afterall. The devs have put a lot of effort into developing their personalities, backstories, and character arcs. If they're going to kill them off, I'm willing to bet its going to be either a very emotional moment, or it's going to be because they reached their crisis point and have turned on you.