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Managed to hit just the right keywords on Google to find it. It's a trilogy by Glen Cook released as Doomstalker, Warlock, and Ceremony in the mid-80s, but these days published as a single collected edition called Darkwar. Note that this would be the Darkwar Trilogy, there's also a Darkwar Saga but that's a different, more recent thing by Raymond E. Feist.
Honestly with titles that generic, I'm not surprised I had trouble finding it.
Really from Jupiter, but not an alien.

I read this probably about 20 years ago, but now I can't remember the title or the author. It followed the life of a girl through repeated upheavals, broken into roughly three parts.
In the first part, the girl lives in an isolated village. The village is attacked by raiders during a harsh winter, with both sides managing to wipe each other out, leaving her the sole survivor.
For the second part, she turns out to have witch powers, so the local faction of witches adopt her and take her to the city to train her. Witch powers are basically capturing and harnessing spirits and using them to accomplish things — larger spirits can achieve greater effects, and your power as a witch is more or less determined by the size of spirit you can control. The most powerful witches can fly into space — where there are much larger spirits than anything on the planet. The largest ones, which only a handful of witches can handle, can be used to travel between stars. Naturally, the protagonist eventually reaches this level, with the plot of this section revolving around her growing in power and eventually facing off against the most powerful witch alive (a member of an enemy faction), who she is able to defeat despite being weaker (at the time) by outsmarting her.
The last section happens when she, during her interstellar travels, encounters aliens that travel through space using technology rather than using spirits (either heavily implied or outright stated to be humanity, I forget which). They end up coming into conflict, with the witches being individually more powerful, but the humans having much greater numbers. Over time, the number of FTL-capable witches dwindles, and it becomes clear that they'll lose if things continue as they have been. By now, the protagonist is an old woman, and feels increasingly isolated from society as witches have become less and less relevant to daily life (since they've been off fighting in space).
In the end, she gathers up all the remaining FTL-capable witches for a final confrontation with the enemy fleet. They approach within striking distance, and then all release their spirits, effectively committing mass suicide, as a demonstration that they want peace between their civilizations, with the understanding that their time had already passed and their society was moving on without the witches regardless.
Edited by NativeJovian