the magical energy of Zeal (the kingdom, not just the queen) came from the Mammon Machine, which took energy from Lavos, right? (i don't remember since it's been a while since i've played CT)
if that's true, then i think the dark energy of Lavos is enough to 'taint'
EDIT: i forgot that this was the Magus thread, so i'll say it now
The masamune was forged from the Dreamstone, which existed before Lavos (the entity's version of the Frozen Flame?), and Magus' power originated from Lavos, so the Masamune (a sword from the entity) could weaken Magus' magic power, which was Lavos'. However, i think that the game mentions or hints at Magus' power's being much stronger than normal Zealians', and grew mainly after being away from the Mammon Machine and Lavos' magic, so it's possible that Frog's using the Masamune to weaken Magus' magic (which is required storyline-wise, right?) could've 'purified' Magus of Lavos' energy, thus making the Masamune not especially effective against Magus when you can fight him again