Islam abhors "paganism" (i.e. non-Abrahamaic faiths and politeists in particular) as much as Christianity does. Just compare the number of Christians in the Middle East today and those of Zoroastrians. The only time you see Islam trying to get along with politeist faiths is when there are too many politeists for a forced conversion to work: India, China, etc.
In the New World you have peoples whose warfare is not up to par with the Old World by 3000 years, and that are going to drop of by 90% in the first generations after contact. Not exactly an India situation.