Furniture, Wood and Cabinetry Finishing - Whether to "spot" re-stain or paint over a problem

I've got a den that has eight 12' false beams. They are boxed pine, and were stained with a dark walnut (or something similar) stain many years ago. Evidently, the roof in the room leaked and water-stained the beams in spots. I'd rather not have to go through the mess and exhausting work of stripping all of these beams and re-staining. I'm not looking for a "perfect" job, but would just like to make the beams a little more presentable. Is there a way of "spot" fixing the water stains, or would it be better to just lightly sand and paint them?
I'm pretty much open for any suggestions.

If the watermarks are black, they aren't coming out easily anyway. The black stains are in the wood, not the same as white watermarks are in the finish. I would consider scraping off the finish where the black stains are located and wiping the area with bleach 10% in water to kill the mildew, rinse, and let dry. Next, I would paint the beams. Clean the beams thoroughly with mineral spirits to remove all the grease, grit, and grime. Lightly sand, prime, and paint.

Hope this helps.