I also disagree with the use of any kind of tomato in baked beans. I was very surprised when I saw even the little bit of ketchup in the recipe of my mother's that I posted. Fortunately, the amount she used was so small, I never even noticed it. If I was making that recipe, I think I would leave out the ketchup.
My own version of Boston Baked beans is meatless, and is done on the stove top instead of in the oven, so I don't really consider it "baked" beans. This is how I make it...
Fry up some chopped onions (one very large, or two medium) until they're caramelized
In a saucepan, put two cans of navy beans (or two cups of navy beans cooked in a pressure cooker)
Add the caramelized onions, a lot of molasses, some salt, and some margarine
Simmer on the stove top until the beans have absorbed the flavors and the liquid has reduced to the proper baked beans consistency