If you want old industrial architecture in a reasonably safe area, go to Hamden (a Baltimore neighborhood, located along I-83, best exit- Coldspring Lane). Go down Falls Road a little ways, then drop down the hill. A good number of the old mill buildings in the Jones Falls valley are still standing. Hamden is still a blue-collar working class neighborhood for the most part, and relatively safe/clean. It is experiencing some gentrification, but it hasn't entirely lost the old feel that made it famous. I'd be careful about going out Eastern Avenue into Highlandtown. It isn't as safe as it used to be. As a general rule, actually, unless you've got someone who is really familiar with Baltimore to escort you, I wouldn't wander around much. Most of Mount Vernon (the neighborhood around the Washington Monument on lower Charles Street) is ok, but it transitions REALLY fast (don't go west of Howard Street!). Do NOT go over to the Johns Hopkins Hospital area - urban war zone. Druid Hill park is quite nice in the daytime - there's a lovely reservoir with terrific city views, and some interesting monuments scattered through. Also in Druid Hill park is the Rawlins Conservatory, a lovely Victorian greenhouse structure which is usually pretty quiet and easy to set up and shoot inside. Mount Royal Avenue up through Bolton Hill, past the Maryland Institute College of Art campus is very picturesque. There are still some old city market buildings in Baltimore that can be visited and are worth a look, but i don't know how well received photography inside will be- some of the merchants will probably think you're a health inspector and will want to throw you out. The Johns Hopkins University main academic campus (on North Charles Street, NOT the medical school campus in East Baltimore) has a fair bit of interesting architecture, including the Homewood house, which was built in 1800.
If you'd like some company/tourguiding, let me know when you'll be in town and I can make arrangements and try to round up a few of the locals to do an excursion up that way.