On the surface, Wilkis agreed to Thalia's request. This was the most he can do at the moment.
Thalia is strong and dangerous, but she is not relentless or hard to talk to like before. With this small exchange as a precedence, there was a chance to rectify the relationship between the two parties.
This was why Wilkis, even if he didn't wish to, he chose to agree to Thalia's request.
And he knows that promises don't matter much in this world, but he still placed his belief in her. Not to mention, if these negotiations fail, then Thalia might not be as forthcoming as before and might take actions against those active soldiers away from Riber city.
As for the problem with Alfin, even though Wilkis didn't wish to accept it. He was a lost cause without any potential left in him anymore.
It's hard to fix a broken mind and Alfin was broken since the day he regained clarity in this world.