Then again, maybe they didn't have good reason. Baybe does not establish anything. Define Good Reason by their society and rules.
Truth is, we don't know enough about that conflict.
There are tons of reasons of to oppose a Luddite philosophy: less needless labor, better standard of living with technology, etc. If I was living in a Ba'ku village and I had to live in some medieval village while other people got travel around the universe in star ships, I might be upset too. I would begin to think Ba'ku society was reactionary and flawed. Why should everyone accept that such a philosophy is good for everyone and not try to oppose it if they think its flawed?
The fact that we know nothing about the rift between the Son'a and the Ba'ku hurts the story. The Ba'ku having the right eject the Son'a from their planet and the Son'a not having that same right looks hypocritical.
How this story supposed to be an effective moral dilemma when the Ba'ku are supposedly perfect and the Son'a are one dimensional cartoonish villains?
What we DO know is that the Baku were being forced out of their homes, that they had lived in peacefully, bothering nobody, for hundreds of years.
It was a society, in and of itself. A colony from elsewhere on inception? Irrelevant morally, if interesting.
Until the Son'a and Federation situations, it was very productive to live there without depending on their technological knowledge.
Being where they are, and hard to reach, unnoticed, made more sense given their origins.
If the Ba'ku were peaceful, how did they force the Son'a off their planet in the first place? It seems like there a lot of holes in this story.