You're confusing separate issues.
set_pos() was not removed, it was changed to use the
position member variable. All Node2D-derived nodes can now use
position = Vector2(x, y)
to set position.
RigidBody2D behavior has not changed. It was never a good idea to set the position directly.
Why not send a signal and/or call a function on the target body to tell it you want it to teleport, and then it does so in its