With eight main characters already existing (MC and seven LI's), plus Elara as a possible extra LI, along with two antagonists (Riven and that electrodick guy), there are already eleven relatively important characters to follow in total. And I'm thinking there will likely be more antagonists on the Andromeda side of the wormhole. Oh, I guess we should also mention that one of the LI's
has dual personalities. I've heard some good arguments that there should be at most seven important/main characters in a story (ST:TNG found its stride when it went from eight to seven characters by killing off Tasha Yar). So the story is already quite full I think, and editing these five unneeded characters out to streamline the narrative branching is objectively the right decision.
And while you may think that it's easy to keep up the passion for a project like this, the number of abandoned games on this site that started off with big ambitions – a large set of characters, huge worldbuilding, complex character personalities and motivations, complicated point systems for different personality traits or sexual kinks, etc – is unfortunately far too numerous to count. The KISS principle has proven itself time and time again to be an absolute and undeniable law in the world of AVN's.
I wonder if the idea that there was "overwhelming negative feedback" might be some type of recency bias on your part? That's not how I remember the last week or so. Almost all of the vitriol I read was people arguing over tag definitions, or others arguing that they each knew better what the dev was planning/hiding from us (mind readers were everywhere). Not really productive comments there, and many of the debates belonged in other threads. To be honest there have been far larger blowups over a game's sudden change in direction (that I won't even mention years later, or else they'll probably quickly derail this thread and give the mods extra work removing more posts), so let's keep this all in some perspective. The drama I saw was honestly minimal and quite easily ignored.
Also, please keep in mind that a lot of activist-minded people exist online who absolutely love to troll these forums.
Especially when the game is one that is popular with guys. You may be able to spot a few of them when they seriously try to talk about "Heteronormativity", "The Evil Patriarchy", etc, anywhere in their post history. So take at least half of the: "We're all just terrified of other guys stealing our waifu's!" claims with a huge grain of salt. Most of the "negative feedback" you're seeing is just hilariously disingenuous attempts at trolling.
Lastly, if you read the dev's communication, how this change is going to play out has been pretty much finalized. A 0.15 hotfix is coming shortly to fix bugs in the initial release, and in that version the five new characters will simply be removed. So they will never exist, and will not need to be killed off, left behind, or anything.
As to the function those five might have served in the story, that's pretty easy to resolve from what I can see. The crew are traveling to the Andromeda Galaxy through a wormhole. You don't really need a dedicated pilot for that trip. A galaxy is a pretty big target after all, so it's practically impossible to miss.

The AI can handle that simple flight, or Talia/Veronica can reveal she has some minimal piloting skills. Amina already takes care of the science/engineering side of things, so no need for an extra "quantum analyst". Talia and the MC can handle the security/fighting when that is needed. And that's it. Problem solved.