Ishikawa said she had to rewrite the first draft because it didn't put the pieces of the plot together in a compelling fashion. I don't think that's the smoking gun you're looking for.
After a whole expansion where he's the antagonist, and then his long, drawn out epic death cutscene followed by an emotional scene with him saying "remember us", it would have been a bigger fake-out death than anything the Scions ever had if Emet just randomly showed up alive just because he's popular. His popularity already led to his return in Elpis and his narration of EW and that was already more than expected.
I'm not sure how getting a scar equals consequences. Either way, it was very obvious retroactively that they wanted all of the main characters together for the climax of EW at Ultima Thule and considering that entire zone involves 0 fight scenes, there was nothing going to happen during that. I'm not sure what they could have done through all of previous EW stuff to give them an injury that gives consequences and still have them show up for the climax that wouldn't be treading ground they've already done. They already had Y'shtola get sliced up and require immediate healing magic which cancelled out any consequence from her injuries except "Zenos bad and dangerous" and make it so the writers don't have to deal with Y'shtola for the rest of the expansion.
Like I said, Zenos slashing another Scion who would just end up getting healed so they can show up at the end wouldn't have added much since it's already been done before. Zenos in WoL's body shooting a Scion would certainly be shocking, but these forums already went crazy over the fact that WoL was being controlled at all and for something like that to happen wouldn't have gone down very well. Jullus injuring a Scion would sour fan's disposition towards him and it's obvious they plan to bring him back for more. A random Terminus creature injuring someone wouldn't have the same impact as a named character doing the same. And there's no way they'd have a Lopporit actually injure someone badly. That's pretty much it for points where I could've seen something happening.
But there's still moments that show us how much is at stake and show us where we failed. Everything that's happening is because our WoL exists and Zenos wants to cause bad things to happen so that we will get angry and fight him again like we did that one day on top of Ala Mhigo. So everything is already indirectly our fault. And then we kill Zodiark which makes it worse and leads to a leader getting eaten and a child being stomped on, which is one of the hardest scenes to watch in the whole game. The Garleans don't trust us and due to their propaganda would rather die out in the cold with the monsters and that's exactly what happens and we fail to foresee it or prevent it. The Twins' failure to convince their father that they're competent and know what they're doing leads to Sharlayan not lifting a finger for us until the very end.