Well I've read Hanta Yo twice and thought it was wonderful. But it certainly didnt lead me to suppose there's anything offensive in the predictable but quite witty 17th century sentiments of Tobacco is an Indian Weed. The song has nothing to say about Indians(or Native Americans) or indeed about weeds. It is just a string of thoughts occasioned by considering the life and death of a plant, the fact that smoke rises towards heaven,the fact that burning leaves ash and tar behind and so on.
   I don't think "weed" is offensive anyway. It is an ironic use of a word habitually used to describe a useless plant, recognising how extremely useful tobacco is. The same term is used for matijuana for the same reasons.