A book titled "Black Indians" provides an very interesting look at the extensive interrelationship of these two people. Yes, the Cherokees held "slaves" prior to the Trail of Tears, but their idea of slavery was a far cry from the way it was practiced by whites. Blacks, many of them runaways, were treated as people, not property, and intermarried freely. This infuriated southern whites, who saw it as a very bad example for their slaves. Most tribes in America had traditionally treated blacks well, providing refuge and resisting all attempts to force them to return runaways. This challenge to the slaveowning system could not be tolerated by white slaveowners, as it threatened their business practices.
This attitude toward blacks changed in the Indian Territory, where a Southren attitude toward slavery began to take hold. This had already begun to split the tribes before secession, and they enlisted on both sides in the war.