It's interesting in Naruto how Kishimoto uses the actual historical ninja culture. The stereotypical ninja image comes from Japanese fiction written over 100 years after ninja villages were either wiped out or forced into the samurai class. The real historical ninja were literate, educated, armed, semi-independent peasant villages.
Yes there were real ninja villages, they also elected their leadership council from the elite members of the clans, and that leadership in turn elected the village leader. They were very (emphasis on very) loosely allied to various Daimyo. The Koga and Iga villages are the best known of the historical ninja villages, but there were numerous smaller ninja villages. They are first noted in historical records in the Kamakura period (1185-1333), but certainly go back further. Back to the ealiest historical records there are more scattered references to similar groups of independent families or possibly small village compounds, these appear to be the precursor of ninja. By the Kamakura period they had organized to full fledged villages, and did indeed train and rank their ninja with the same three levels you see in Naruto: Genin, Chunin, and Jonin. There was also near gender equality in ninja villages.
Now, unlike in Naruto, the actual historical ninja rarely were involved in major battles- although it's known the Koga and Iga villages did fight in battles alongside samurai in support of the Daimyo. (likely the smaller villages did as well). The pre Kamakura period proto ninja groups seem to have more involvement with actual battles and don't seem to have ties beyond their own people. The historical ninja actually did far more spying for hire than fighting or even assassination for hire. (Both male and female ninja)
Kishimoto is now showing the prehistory of ninja villages in Naruto's world. (I love how Kishimoto has gradually revealed more and more of the pre chapter 1 history as the story has continued- the manga is still in the top 5 manga in both Japan and the US after 13 1/2 years publishing history in Japan and 10 years in the US, so clearly this moving backwards and forwards in the fictional world's history has been engrossing for the readers.). There's always been far more to this manga below the surface (something readers were clued into early on when Kakashi tells a young Naruto, Sakura, and Sasuke to "look underneath the underneath". Indeed.
Hashirama's flashback story is giving us a fuller image of the pre ninja village world than the brief references we saw prior. This is basically Kishimoto's speculation about how those historical proto ninja families became ninja villages. Hashirama's father is just as cold and brutal a man as Madara's father. Young Hashirama is full of idealism- wanting a better world and showing even at around 12 years old or so, the village system he later initiated (as an adult) be was already taking form in his head. I'm hoping we'll get insight on Mito and Hashirama's meeting and her choice to go with him and believe and support his dream