Hybrid structures of quantum spin-Hall insulators (QSHIs) and superconductors (Ss) present a unique opportunity to access dissipationless topological states of matter, which, however, is frequently hindered by the lack of control over the spin polarization in QSHIs. We propose a very efficient spin-polarization mechanism based on the magnetoelectric (Edelstein) effect in superconducting QSHI structures. It acts akin to the Zeeman splitting in an external magnetic field, but with an effective $g$-factor of order of 1000, resulting in an unprecedented spin-splitting effect. It allows a magnetic control of the QSHI/S hybrids without destroying superconductivity. As an example, we demonstrate a recurrent crossover from $Phi_0$ - to $Phi_0/2$ - periodic oscillations of the Josephson current in an rf superconducting quantum interference device ($Phi_0=h/2e$ is the magnetic flux quantum). The predicted period halving is a striking manifestation of $0-pi$ Josephson transitions with a superharmonic $pi$-periodic current-phase relationship at the transition. Such controllable $0-pi$ transitions may offer new perspectives for dissipationless spintronics and engineering flux qubits.
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