There are a lot of nasty encounters, but they are widely spaced out. If you let the PCs explore and retreat, explore and retreat, they should be able to handle things.
However, it would be more rat bastardly to have the evil leaders begin taking action against the PCs. Example, after the PCs defeat the Terrible Iron Golem, wouldn't the evil leaders want to respond to such obviously dangerous intruders? I know I would! Reinforce key positions, increase the frequency of patrols, maybe even abandon certain indefensible areas.
It may also make sense to have one of the warring factions attempt to co-opt the PCs to their efforts - this would be the NPCs approaching the PCs, not the other way around. Of course the NPCs will withhold certain key information....
Finally, I would role-play Eli Tomorast as paranoid in the extreme. He's already died once, and he doesn't want to die again. At the first hint of trouble, have him use maximum lethal force against the PCs - sending minions to assassinate them, constantly scrying upon their progress, casting long duration spells to impede their efforts, etc. That would make him not only a nastier villain, but one whose ultimate defeat is that much more satisfying.
