as far as I know, salt is only added at the end of cooking (to avoid beans becoming tough).

Yes, you can. The cooking instructions from Rancho Gordo beans says it's ok. The Splendid Table says it's ok. Shirley Corriher says it's ok. Salt toughening beans appears to be a myth.

HalfPint, I know there's debate favoring salting during the soak, but I haven't seen it for the actual cooking. I haven't checked out Shirley Corriher, but is on the Rancho Gordo site today:

"While the beans are cooking, leave them alone! Don't add tomatoes or salt or keep stirring them. Acid and salt will keep the beans firm and should not be added until the end."

this debate is right up my alley, but I guess as a person who always salts their dried beans (otherwise they are bland!), I could have made my question a little clearer-- could the baking soda interact with the salt in a weird way?

It seems to me that bean cooking is more art than science, and I can easily believe that two different Rancho Gordo writers could disagree. Here's what Harold McGee says in On Food and Cooking (paraphrased):

In the soaking water, sodium in salt displaces magnesium from cell walls, making them more easily dissolvable, and so cooking times decrease. But in cooking, salt slows the rate that water is absorbed. So beans cooked in salted water eventually get done, but it takes longer. And since salt reduces the swelling and "gelation" of starch granules, beans cooked in salted water can taste a little mealy.

Also: acids make cell walls more stable and less dissolvable--hence, no tomatoes. Sugar reinforces cell walls and slows swelling of starch granules--so, no molasses for Boston baked bean fans? EXCEPT that with long, slow cooking, like for Boston baked beans, the acid and sugar help keep the shape of the beans. They do get done, just not quickly, but that's part of that tradition.

And of course, the other generally known truc: when beans are taking forever to cook, a pinch of baking soda helps dissolve cell walls. But too much baking soda tastes funny, so just a pinch.