I would have left it.
I have an orange hab plant that has some enormous pods. The shape of the pods also are not the typical shape (definitely a cross) but it looks cool and we can't wait to taste them. It sure makes for an interesting conversation piece.
Our elementary school garden has 6 raised garden beds. One of which ALWAYS gets diseases on its pepper plants. We can tell when it is going to occur because the leaves start to look brown and spotted (a type of mosaic virus maybe?). The branches eventually turn brown and snap off very easily...