Looks to me like Guinan was aware of all the good reasons mentioned here
not to be on a warship but the only one in this alternate reality to really understand it.
Theoretically the whole situation could have been Q's little revenge to what Guinan did to him earlier:
DATA: The Captain and many of the crew are not yet convinced he is truly human.
GUINAN: Really?
(
So she picks up a fork and stabs it into Q's hand)
Q: Argh!
GUINAN: Seems human enough to me.
Certainly, Q would have had some fun watching Guinan how she desperately tried to explain the situation and get out of it.
Guinan arrived with other refugees in ST VII so she could have meet Picard somewhere else at Starfleet in the alternate reality.
But that eventually depends on how you'd like to interpret this little dialogue from BoBW, IMHO:
GUINAN: ...
Did he ever tell you why we're so close?
RIKER: No.
GUINAN: Well, then let me just our relationship is beyond friendship, beyond family. And I will let him go.
I'm not aware that this was ever explained, but it's obvious that Guinan considered the possibility that Picard told Riker but would never do so herself and probably because it could damage Picard's reputation in the eyes of Riker.
It has since become my pet theory that during their idle time in the cavern in "Time's Arrow" Picard actually told Guinan about the Borg assimilating her people and planet in the 23rd Century, so she would have an advance warning that eventually would bring her back to Earth in ST VII.
If the alternate reality Picard never travelled back in time to give her that warning, chances are high she would have never escaped the Borg and therefore not been able to serve on any starship at all.
Bob