I understand on "the Native American problem" he was faced with an untenable status quo and even worse ideas from the states in question. However, solving it by negotiating with largely unrecognized leaders, then forcibly relocating ethnic populations across the country in exchange for dubious reimbursement for their native and sovereign land doesn't exactly seem a moral solution.
It certainly could have gone worse had the states had their ways, but his solution wasn't exactly a paragon of ethical behavior.
So she's a former slave, a liberator of slaves, and a plantation owner and owner of slaves all in one. Would having her on a bill be in poor taste? (Granted, there are probably more prominent persons who should be on a bill before her.)
(I once dated one of her descendants.)