My constables actually talked about this and arrived at the conclusion that, while Ekossigan's goals more or less chime with their own, they cannot let him live for three reasons: 1) He is a murderer, killing a boy and the druids at the orphanage, and 2) the king ordered them to execute him as a favor to the Unseen Court, as requested in Asrabey's mission – no matter his guilt of any crimes, his methods, his goals, whatever, and 3) Gale is one of my PCs' love interest... and he didn't take kindly to her effective enslavement.
Now would I have had Ekossigan listen to the constables if they had decided to try and ally with him? In general, sure, why not. He is already far gone by the time the party can encounter him, of course. But in my view, Ekossigan simply feels misunderstood and let down by the failure of all concerned to see the danger of the Ob's conspiracy. I would probably have had him jump on any allies who actually agree with his views, and who promise to be a strong addition to his forces (a team of level 7 PCs is one hell of a crack troop!).
Nevertheless, "my" Ekossigan's madness might have made such a match uncomfortable in the extreme in practice. He would have insisted on going through with the mass sacrifice to bring over a small fey army, so as to ensure success in his mission. He would also have insisted on being the sole commander of the whole undertaking, madly micromanaging all kinds of things the PCs would have no stomach for.
Finally, I might have had Ekossigan turn on his allies once his spring aspect turned into his winter aspect (in effect, as soon as the real fighting starts). As Ekossigan of Winter, he's not the same person anymore, and any kind of hopefulness for a good ending (spring aspect) is replaced by a certainty that the end is nigh and that all living things must die (winter aspect). At least, that's my interpretation of the Season Slain thing.