Aw... it seems the whole stem and mother plant is completely gone

Uhm, I guess the best you can do is to really hope for the best! I have never seen a kalanchoe with so much damage, but maybe if you bury the roots... there is a chance a new little plant shows up. Try to water the plant less, also try putting some little rocks in the bottom of the new pot, so you make sure the plant will have a great drainage.
In my experience kalanchoes really like it when you wait until the soil is really dry... I always watered mine when the soil was really dry, and sometimes I could feel how ''tender'' the leaves of the kalanchoe plant felt to the touch. That was a clear sign they needed some water. After that they looked as happy as ever
Best of luck with your kalanchoe! Keep us posted!