I liked the Section 31 reveal simply because it gave Reed something
interesting in his background. "Stuffy guy with lots of allergies and phobias who likes to blow stuff up" is pretty weak.
Sure, in an ideal world the writers would have come up with the idea during the series' conceptual phase so that it could have been a part of Reed's development from the first episode. But it wasn't. IMO, adding it in even in the late stages of Season Four did more good than it did harm.