Respectfully I disagree with pretty much all of this. First, I think Ginger Island is an incredibly cool and successful expansion which adds a ton to the game, and I'm a huge fan of it. I'm so glad it was made, I was shocked that such a huge patch was just rolled into the base game instead of selling it as an add on or expansion, frankly the latter would have been absolutely justified. I suspect the reason he didn't go that route is because the success of the project has already been beyond his wildest dreams and he both wanted to do something great for everyone who has supported him and make future patch management much simpler by not having diverging builds for those with or without the expansion.
Setting aside the fact that I'm glad it's part of the game, I also disagree with pretty much all of the characterization. You aren't "conquering" the island, there's no one to conquer it from. Leo is a shipwreck survivor, and Professor Snail had his life saved by you and his research completed by you while otherwise being totally unimpacted by your presence or the development done. Secret Lairs are cool too, and Mr. Qi never did anything to harm anyone which I'm aware of.
And as far as the "realism", while I pretty wildly disagree with how realistic anything related to Ginger Island is, in virtually any way (how is there a functional forge just chilling in the middle of a volcano; how are all crops able to be grown without any weather or seasonal limitations at all; how are there these magic birds that eat these scattered but discrete walnuts and do major construction work in return; I could go on and on), I don't even agree with your characterization of what is a purportedly "realistic" sequence of events, of conquering islands and natives all but disappearing etc. I don't know who the "we" is supposed to be which is taking natives captive or killing them off but it certainly doesn't include me. Furthermore, there's no populace which is truly "native" to an island, by the very nature of islands. Just like Leo, they all came from somewhere, just a question of when. And when they settled there, they did so exactly for profiting off the land for comfort and material wealth, inherently island-settling folks are explorers who found something there worth putting down roots. Beyond that, coming into conflict with other sailing cultures and warring over ownership of islands is a part of history generically and is hardly limited to one group or ethnicity.
So, tl;dr, no, none of that is right in my opinion. Not in terms of the merits of Ginger Island as a part of the game, not in terms of its characterization of the events of Ginger Island, and certainly not in terms of the 'realistic' events it purportedly parallels.