I have a small pair of side cutters that clips them close, and as Rip said don't worry much about it. That end will fall inside the bead, and rarely comes back out. I also have one of those little cement bottles with the metal tube, and a drop of head cement inside the bead makes sure it doesn't come out. They don't rattle, but for most bead chain that I use, I doubt any rattle they might have contributes much to the fly anyway.
I also try to only use stainless steel or brass bead chain because they're both a better choice for saltwater applications and rather than have to pick & choose, I just go with them for less concern since I tie flies for both freshwater & salt. However, some of what is sold for tying is steel, and if using them for flies intended for freshwater, it's not a big deal, as the fly usually gets destroyed before there's any issue with the metal. I have had the steel bead chain rust, and stain the materials, and not something I care for.