I don't get this argument. Him coming back doesn't undo his sacrifice.
It kind of does... because... he didn't actually die. A sacrifice only really works if something is lost. But... i'm also not particularly zealous about this. It's fine.
The real damning point to the idea of Confederation-Past-Guinan being distinct from Federation-Past-Guinan is that Federation-Present-Guinan remembered everything that happened in the past in the season finale. So does Federation-Present-Guinan also not remember "Time's Arrow" because she's actually Confederation-Past-Shimed-To-Federation-Present Guinan, and all pre-2024 time-travel in Star Trek post-Picard has been replaced with similar but distinct Confederation versions? Does Confederation-Past-Guinan suddenly remember, "I already met that old guy when I was hanging out with Mark Twain," when team-Picard averts the Confederation timeline and she becomes Federation-Past-Guinan again?
Now *THIS* is the better question.
I can comfortably put this in the "Q did it" category. This wasn't "normal" time travel... any of the normal rules can be thrown out the window. We've never seen a consciousness time travel independent of its body, inhabit a body in a different timeline, time travel to the past, and then return to the original timeline still in the body of the alternate timeline (which also means... shouldn't Prime Timeline Picard still be there when Confederation Picard Body shows up?)
This is all Q rules now. Q made this time travel happen. Q sent everyone back. Q let Guinan remember what happened in both timelines... Or it might not even be Q chicanery and just El Aurian chickanery... she might remember the S2 events and the 1895 just by virtue of being El Aurian.
EDIT -
*OR* a third option is that actually yes, Picard was always in 1895. Guinan was suffering from the timeline sickness. She wasn't at 100%, it's been established that the shifting timelines can have a dramatic effect on El Aurians. She may not have remembered Picard from 1895 just because he timeline-senses were all out of wack.