If we're to assume that Eve tells Cassie what he said when they're talking things out on Day 5, then it's hard to see how him saying, "But I think we should simply tell her", is a worse response than, "This morning was very difficult to handle". Both responses would seem to indicate that he doesn't like going behind Cassie's back and the first one even makes it clear that he wants to tell her, so why would that first response be enough to send her on a downward spiral and lead to the bad ending? I honestly don't think it makes any sense.
I agree that giving the second response here is counterintuitive. But, it's only required if you don't give the "I don't accept it" response at the end of day 4. And, talking to Cassie instead of messing around with her on day 4 is supposed to be required, in order for the good ending to be possible (it's a bug that it's not right now.) Which means you'd always get the option of giving the "I don't accept it" response. And, in that dialog, it does seem to be the better response if you want both of them. So, from a gameplay perspective, there is a clearer route available.
As for the "does it make sense" perspective, I think you're looking at it from the wrong angle. Requiring one of these 2 responses aren't about how they make Cassie feel, but how they make the MC feel. They're required in order to get the "I choose neither" option. They establish that the MC does not want to choose one over the other, he'd rather be the one to suffer in order for Eve and Cassie to stay together.
In the first case, the conversation for "simply tell her" implies that you're doing that in order to end things with Cassie and continue with Eve. The one for "difficult to handle", she suggests choosing Cassie and MC says "fuck it, I'd choose neither before that". Basically, in both conversations, the first choice is the MC saying "I'll choose you and Cassie will handle it" and the second is "if you don't let me choose you, I'll choose neither and be the one that's alone."
And, telling Cassie you'd rather choose neither, to hurt Eve and her less, is what leads her to the conclusion that that still wouldn't work, everyone would end up hating everyone, and there's only one better solution. Because MC never says he wants both, he doesn't even consider it a possibility, that's all Cassie's idea.
Edit: note, I do think the gameplay side of getting the good ending is still a tiny bit tough, like there's no clear indicator that anything you did was massively wrong or would lead to such a drastically different result. I am not easily emotionally disturbed so it didn't bother me, but I understand it could bother some. My only idea for solving that would be, at the start of day 5, if you're doomed to the bad ending, get a trigger warning screen saying "play on at your own risk or go back and try to fix things if you don't wanna see it." But, well, Bioshock didn't give you any warning
before your character beat an old man to death in first person, nor did Dragon Age Origins
before any of the multiple things there, so telling people to suck it up it's a game and sometimes they'll shock you is also a valid response in my opinion.