If it was just about power though, you would think that if you give him the stones then he would betray you and dominate the elder brain. He doesn't though. If you trust him, he does exactly what he says he'll do and there are zero consequences.
Ultimately, he wants to live. He only kills Ansur because Ansur tries to kill him, he wants to destroy the Elder Brain because it's a threat to him, he doesn't want to free Orpheus because he thinks Orpheus will kill him, and he joins the Elder Brain when he thinks he's no longer able to defeat it. I don't think that's a particularly evil motivation. He never lies to you, never threatens you, never charms you, never dominates you, and never betrays you. He's the only reason you're alive and he can kill you at any moment by rescinding his protection. He never even floats with as a possibility to you though.
It's unfortunate that siding with him shafts Lae'zel.
He never lies to you? Really? That's a bit rich considering that he comes to you in a disguise that was deliberately made to fool you. That is pretty much the definition of a lie. He also lies about Stelmane and he does threaten you if you treat him badly. Sure, he protects you with Orpheus' powers but that is only because he needs you i.e. someone outside of the artifact to work towards his plans of liberation from the Elder Brain.
So, does he have good intentions? Not really. His intentions are only as good as his nature - which, as a soulless parasitic braineater, is still pretty bad all things considered. Acting out of self-preservation might be neutral when viewed in a vacuum, but given the context of what he's preserving i.e. the existence of a mindflayer that eats human brains and enthralls people, it doesn't seem so neutral after all (which is what Ansur recognised as well).
People say "oh, but he doesn't choose to betray you and dominate the brain instead of destroying it" like that somehow means he's a good guy. What it really just means is that he's not bad enough to seek out total world domination (low bar) or maybe he suspects that if he went down that route, enough powerful factions would eventually come after him to guarantee his demise. Maybe he knows that if the three chosen of the Dead Three failed, he would also eventually lose control over the brain which after all is the one who possesses all the power of the Crown. Anyway, the absence of total evil is not proof of good character.
What's far more interesting is that when faced with an actual moral dilemma in the case of Orpheus, he never even tries to hedge his bets by entertaining the possibility that Orpheus might help out and instead opts for the nuclear approach of siding with the brain if you don't want to doom the Gith for his paranoia. He has the choice between the possibility of death or guaranteed subjugation and he instantly chooses the latter. Now, of course he doesn't have player knowledge and the whole scene is mostly a plot contrivance anyways but it still tells us enough about the character to not feel even a little bit bad about siding against him.
