I believe that Gillis is being genuine about Manny's eye and not just doing this because Kesler/Booth came back. If they had no hesitation to waive Volpatti for no apparent reason, they would've done so to make room for Booth (since Ebbett went down for Kesler).
That said, I get where Manny is coming from. Obviously it's tough to just have your career taken away like that, so he'll probably work as hard as he can doing whatever he can to get his eye back. And I'm sure the Canucks would love nothing more than for that to happen and would re-sign him instantly (at a discounted price for a discounted role).
Even though it's Manny Malhotra, if it was an issue with his performance, I don't see why Gillis wouldn't just trade him or waive him, and straight up say that he isn't fitting a role on this team right now, but we wish him the best and have a organizational job in the front office/coaching staff for him any time he wants. The concern is genuine, and the reaction from both sides is genuine.