That's fair. My hope is that the fight with Borys would be so taxing the party was on their last legs and finding that Rajaat had withered is a welcome anti-climax. They've done the hard part, finishing off the monster that began the cleansing wars is the victory lap. But it's definitely something you'd have to thread the needle with.
Yep. Your resolution is actually really nicely poetic in a lot of ways and I do like it. The devil would be in the buildup though. If the PCs are fighting Borys - why are they doing it? How much do they know about Rajaat at this time? Have they decided to fight Borys on the assumption that Rajaat can't be worse, or have they done it in the full knowledge that even if they win, they'll quickly have to finght Rajaat immediately after (that latter course of action would demonstrate ... no shortage of self-confidence, if nothing else!)
From vague memory, in the novels the main characters got duped by Rajaat's servants (the shadow giants and Rajaat's loyalists sorcerer-kings Sasha and Wyan) into proceeding down the path of freeing Rajaat, but by the time they fought Borys they knew the truth. I don't really remember why they ended up doing it (I suspect it was a combination of 'they're all impulsive meatheads on both sides' and 'it was scripted to happen' because Cerulean Storm is unfortunately not a very well-written book and character motivations went out the window a bit) - but PCs can't be relied on to make that same decision if they're in the full knowledge of the facts. And if they're not, then they probably have very little reason to kill helpless Rajaat at all once Borys is dead.
Exactly. It's a choice between "the worst, most genocidal dictators in human history collectively" or "Aliens will literally exterminate all life on the Earth, yes, even deep-ocean life."
When people like Stalin are the better option, when pragmatism says "well, we can let the genocide slide this time", it weakens the message that these people are absolute monsters.
If I'm retconning it all for a modern-day reinvention of the Prism Pentad in adventure form, then I'm going to probably rule that when Borys and the sorcerer-kings overthrew Rajaat and discovered that they couldn't kill him, they got the reason wrong. They assumed because they were the most powerful remaining creatures in the world and they couldn't kill him, the conclusion was that he couldn't be killed. They were wrong. He couldn't be killed
by them. The sorcerer-kings are, after all, Rajaat's creations. He made them, his magic infuses them, their power is his. They were able to turn against him, but they couldn't unmake the power that created them. So they locked him up, and established themselves as tyrants, and spent centuries reinforcing the bars of his prison with the souls of innocents and claiming justification for their deeds.
You cannot defeat tyranny with tyranny; you cannot defeat Rajaat with his own power. Rajaat can be defeated (it wouldn't be EASY of course) by other powers than his - preserving magic, druidic or elemental magic, etc. The sorcerer-kings in their arrogance never considered this, and if Borys ever contemplated the possibility in his centuries of brooding and research above Rajaat's prison-coffin, then the little bit of Rajaat that lurked behind his eyes would subtly turn his thoughts aside.
The immortal genocidal dictators cling to power in order to contain Rajaat, but in reality all their wards and protections around his prison only serve to keep out those who could actually finish the job. And Rajaat's power inside them will not let them realise this. The people on top change, but the system remains the same. You can't defeat evil with more evil. You can't overthrow evil by collaborating it, and using its weapons. You need others, outside the ossified brutal established power structures, to truly make change that lasts.
Thematically, this works better for me. You need to offer the PCs a third choice, other than siding with Rajaat or siding with the sorcerer-kings. The novel canon was a mess (despite Lynn Abbey's valiant attempts to clean it up later), and the canonical solution was a deus ex machina that just wouldn't work in game.