Ideology and practicality clash, such is life. From all accounts, he cared deeply for Sally Hemings and her offspring. You must remember, he truly believed that the slaves were not quite 'human.' I'm not saying he was right, not at all, but time and place.
Owning slaves, well unlike George Washington, Jefferson was never wealthy in the larger sense, it was all tied up in land. In order to do what he did, the plantation had to keep going, thus slaves. Economic necessesity, what some have a problem understanding regarding the war of 1860.
The Bank again, a necessary factor, which he was bright enough to understand. Much like the Louisiana Purchase, certainly questionable as far as executive decision, but the correct one.