There could be many different reasons for that, and I wouldn't say that it doesn't make sense that she has a European name.
According to the Wikipedia entry on Mestizos in El Salvador (link below), a lot of marriages took place between Spanish men and Native American women. So the Spanish men would have given their children Spanish names and that is probably the reason for what you are asking about.
https://en.wikipedia.org/wiki/Mestizo#Central_America
I think your friend should just choose a name that she likes and change her name to that. She could easily have ancestors from more than one indigenous group, not just one. It is very unlikely that she would ever manage to trace her Native American ancestors back as far as 700 years.