Personally, I just about always had Frog in my party at this point of the game on a new game play through so he could take advantage of the spiffy anti-mage weapons he gets in the ocean palace. As such, the moment before Crono dies, rather than just say "Crono" like Marle and Ayla do in the linked video, Frog says "Crono, desist!" So I always assumed then that Crono was resisted and fighting against the power drain that Lavos used on Magus, and in turn, Lavos ends up having to obliterate Crono. Furthermore, Crono has a feint white glow during the whole lightning part whereas Magus glows red.
One last thing about the "glowing orb" of question. Not only does it rise up, but once they leave Lavos' shiny blue realm there, the orb has shifted position, and lands on the ground. The landing would be another indicator the object would be physical in nature, so another point for being the pendant.