Injun Joe is essentially a two dimensional character in the Twain story of Tom Sawyer. He is essentially a force of nature, not a person and could be replaced by a large bear, viscious dog or even a flood. In modern movies he would be a zombie, a mindless shambling creature that pursues the hero without thought or reason. If the character of Injun Joe had been developed we might of have gotten an insight into his back story - what made him evil, why he remained in the area of Tom's home town etc. If compared to Frankenstein's monster (in the book, not the movie) he obviously comes out second best as we never understand his motives and never have a shred of compassion for him.
As a result Injun Joe is cetainly a danger, he is not successful as a villain.
No, Mark Twain should not portray Injun Joe as a villain in The Adventures of Tom Sawyer because it perpetuates harmful stereotypes of Native Americans. Instead, Twain could explore a more nuanced and complex portrayal of Injun Joe that goes beyond traditional tropes.
Injan Joe