Sure, I knew about her name being Yoko back then... I read everything just like you probably did. But let me explain.
I'm French, and our edition kept the same names as the original Japanese version :
Ido named her Gally after the his lost cat when he first found her. Desty Nova later on calls her Alita during the Ouroboros arc.
France first got a 9 volumes edition of the original series, including the very first ending.
Before Last Order, French audience also got a second "limited" edition which included a few one shots Kishiro had done in between, such as the "Sweet Night" short stories.
It basically focused on events Ido lived a few months before he found her. It was a very sad and touching story.
This is a scan I did of the first page.
The Gally cat makes a short and symbolic appearance at the end.
I dunno if this was published in North America ?