My point of view is that Mara Jade deserved better than getting killed off in a conflict nobody wants to remember. If there was a time to kill her off, it would've been during the Vong War's last battles, having the bad guy kill her or having her sacrifice herself in some form to give the Jedi an opening to end the war would've been worthwhile. Either that, or I'd just slowly retire her and she spends the rest of her days like Jocasta Nu, rummaging through a New Jedi Library and teaching kids while Luke runs the Temple and the Order like Yoda did. Maybe she goes off on a final adventure as Timothy Zahn planned, and you can have her and Luke go off on a mystic quest and kill Abeloth or fight the Lost Tribe of the Sith while the rest of the galaxy worries about another war. Having the two of them suddenly be made absent would be the perfect time for Lumiya or Thrackan Sal-Solo to start plotting some new conflict to weaken the galactic order.
As for Jacen going evil, it's even worse than Anakin Skywalker going evil. As sloppy as some parts of Anakin's fall was managed, at least there were solid reasons. Anakin had a rough childhood as a slave, the Jedi didn't trust him, his mentor constantly berated him, he wanted more power to prevent those he loved from suffering, Palpatine is his only real father-figure giving him pep talks and advice that he feels comfortable with, and he is increasingly frustrated with the political order of the Republic and already favors a centralized government where problems can be solved swiftly. The seeds of a disgruntled, power-hungry space fascist were already there, just waiting to grow. The man we know as Darth Vader was already within Anakin as early as Episode 2, and he just blossomed down the line as Anakin's problems mounted.
Jacen, on the other hand, had every advantage gift-wrapped and given to him. He was the son of royalty/war hero celebrities to whom the rulers of his age had to bow and scrape to. The Jedi of his time were open and understanding, and the grand master is his uncle, who would do anything for him. He had all the power he needs, to the point where he became one with the Light Side and vaporized the Vong leader with a show of power that neither Palpatine nor Yoda could ever equal in the height of their strength. The new galactic order has him as one of its most trusted agents; both former Rebels and Imperials from the OT era would look upon him as a respected authority.
For him to suddenly fall, go full Space Fascist, and kill his aunt makes no sense whatsoever. At that point, he should've surrendered his will to the Living Force and just become an ambassador of peace, and instead of going full autismo and doing evil things to keep the peace, he would've just accepted that war is part of human/sapient nature and just do his best to pick up the pieces and heal. Jacen should've become the SW equivalent of Saint Francis or Mahatma Ghandi and sought peace for everyone. When the Second Galactic Civil War breaks out, he shouldn't be the Galactic Alliance's Heinrich Himmler, he should be the guy calling for both sides to lay down their arms and talk. Hell, if he was going to die in that war, he should've died in the midst of the first battle, as both sides begin firing upon each other and he's perforated by shots fired by both sides. That would poetically show the lights getting blown out as a new era of darkness starts with a new galactic war that threatens to turn brother against brother once more.
For him to just fall like that, in an even shittier remake of his grandfather's fall, was tired, sloppy, and did not match up with what the NJO novels showed about him when the Vong Saga ended. Sure, I'm more than happy calling the NJO novels derivative and sloppy, but they are at least part of the canon, and future books should've honored the setup that Jacen had by the end of that story, not someone who will veer into the Darkness for stupid reasons, but as a literal beacon of Light that would guide the galaxy to a better future.
For later books to suddenly throw that into the trash and make Jacen into an even shittier copy of his granddad who kills his aunt just reeks of the same tired comic book nonsense where good guys go bad for stupid reasons and love interests get shoved in the fridge for the sake of cheap drama. Not to mention it makes the SWEU seem bipolar about characters and it explains why more than a few of the book fans were calling for a canon wipe before the Mouse bought the franchise. Especially when these books were stupidly borrowing tropes from comics that regularly have retcons and canon wipes because the writers wrote themselves into a corner.