Which president advocated assimilation over direct indian removal?

Thomas Jefferson.

Jefferson was a suscriber to Enlightenment ideas, which had two consequences for the way in which he thought about Native Americans. First, he believed them to be capable of learning and reasoning, and to possess individual liberty. Secondly, it made him think that European culture was the height of civilization, and that Native Americans would benefit from adopting it.

Jefferson used treaties and commerce to continue to get Native Americans to adopt European practices. This "civilization" process would also make lands occupied by Native Americans available for settlements and agriculture. Therefore, from Jefferson's point of view, everyone benefitted.