It makes it all not very enjoyable for me anymore.
That's incredibly sad. It says nothing about Twain, but much about you. For that matter, you really need to read it again. He was writing a satire against Cooper's books, and in this, he was right. If he went to far in portraying the Native American's lack of virtue, and to the white man of the time, this supposed lack of virtue was very real, and often accurate, by the standards or western civilization, then Cooper and others most certainly went too far in portraying their virtues. This is still done today. Whether it's political correctness, or just plain fear, Native Americans are usually presented today as something approaching a Greek God. It's almost impossible to sell something today that presents a Native American as an evil, murdering SOB, even though a fair number qualify perfectly for this role.
Twain was writing from his own personal experience, and there were certainly a large number of Native Americans who fit his profile perfectly, just as there were large numbers of whites who were just as bad.
Twain should not have applied his experience to all Native Americans, but like it or not, he was right about the ones he dealt with personally. For a man who lived where and when he did, I find his views perfectly understandable, just as I would feel the same about a Native American of that time period who applied his experience to all whites.
When you start applying today's sensibilities, which are as inaccurate as were Cooper's, to a man who lived when Twain did, you're simply asking the impossible, and pretending that you would have been any different.