That fungus isn't really an issue. It is, as said, growing on deadwood--which is dead. The dieback you're getting looks typical for what happens with some larger collected wisteria after a couple of years in a pot. It has to do with rot die back underneath the dead portion. I'd bet that dieback goes all the way down into the roots. The plant can abandon some weaker roots in favor of stronger roots on the other side of the trunk, which kills the portion of trunk above the weaker roots.
The plant will likely survive that dieback, as wisteria are extremely strong growers, BUT the end result could take a while to settle, with additional sections dying as well. Best to let the plant grow without any pruning, let it extend and strengthen next year. You can carve out the deadwood--using wood hardener on wisteria wood is mostly useless. The wood is extremely prone to rot and applying wood hardener to it will probably not stop the rot, as it will continue underneath the hardener. The solution to this is to allow the plant to grow well, filling in the carved out sections with callus tissue.