That really shouldn't be an issue barring an unexpectedly dedicated group of players.
I've got a history of being a long-lasting player in games that interest meAlso, I recognize several others here as long-running players as well (Egan) (Cael). So I would actually expect your endurance as GM to be the limiting factor, rather than the player's endurance. GMing always has a much heavier workload after all. In any case, with this player group you actually could easily end up with exactly that kind of dedicated group of players. If you're up for running it for that long anyway.
It could reasonably take over a year to reach notable corruption levels unless you really go whole hog into Chaos, given that a single reasonably sized firefight could take a month in PBP. You can buyoff Insanity for 100 EXP a point and if it ever ends up mattering I can make similar rules for Corruption.
The system's not a big deal for me at this time because I don't have the personal experience with the game, your GMing style, and the story you're planning that would be necessary to know how much it's going to be a factor and how good or bad it actually is, so unless it's completely ridiculous then I don't personally care all that much right now. I was just trying to put myself into Cael's shoes and to try to understand their position. I personally have every intention of staying no matter your decision on the matter.
And honestly part of why it's iffy for me is because it actually breaks me a bit out of the setting since the game's systems make warp travel more dangerous than in the lore.
That last part you haven't expanded on all that much, but you have repeated it and emphasized it, so it seems like it's a major immersion-breaker for you. I do find it odd how the warp can be as rough to use for travel as it seems to be in the ruleset and yet have it still be the primary method used
when other methods do exist in-universe. For example there's some safe shielded warp paths the eldar leave laying around that most imperial ships avoid because they take about twice as long as the more turbulant, freeform, warp travel. There also is the tau method of interstellar travel, which again most imperials hold in contempt. And there's even the simple fact that many imperial ships do not take the calmest path between A and B in the warp, again opting for speed and some turbulence over the safe path. If every time they did this they were increasing their travel risks as substantially as it seems to in the game rules, I don't see how that would the the normal decisions people would make. Hell, there's supposed to be individuals that are lifelong spacers, how would these literal children survive repeated warp trips over and over long enough for them to grow up? If it was truly as dangerous to use warp travel as listed in those rules, then the imperium would have broken down long ago due to logistics failure.
Again, this is my best guess as to what the long-form of Cael's concerns are. I do think it's a valid argument, I don't personally find it compelling enough to deter me, but I'm attempting to voice and sympathize with them, largely because I've enjoyed the games I've played with Cael, and respect their judgement quite a lot. As a result if the concerns were alleviated and Cael felt like joining in, I'd be delighted.