There is a precedent to spirits existing outside of the Fade and outside of a human host. You met him. While I cannot guarantee that Justice would be quite so friendly as Cole, or even that it would choose to manifest in such a corporeal way, it is not as though we are going into this blind.
And he alternative is leaving them joined to one another. Which is to say that Anders and the spirit's comfort trumps everyone else's well being.
As to the Blight, given Justice seems to have been suppressing it, we should have time to work out a solution.