Suppose you have a theory of maps $\phi: {\cal T} \to M$ with $M$ some Riemannian manifold, Lagrangian $$L~=~ \frac12 g_{ij}\dot\phi^i\dot\phi^j + \frac{i}{2}g_{ij}(\overline{\psi}^i D_t\psi^j-D_t\overline{\psi}^i\psi^j) -\frac{1}{4}R_{ijkl}\psi^i\psi^j\overline{\psi}^k\overline{\psi}^l,\tag{10.198}$$
where $g_{ij}=g_{ij}(\phi)$ is the metric, $R$ its riemann tensor, and covariant derivative
$$D_t\psi^i~=~ \partial_t \psi^i +\Gamma^i_{jk}\dot{\phi}^j\psi^k.\tag{10.199}$$
(Details taken from the book Mirror Symmetry, written by Vafa et al., paragraph 10.4.1.)
Taken for granted that the above Lagrangian is classically supersymmetric, with susy transformations given by
$$ \begin{eqnarray}\delta\phi^i &=& \epsilon \overline\psi^i-\overline\epsilon \psi^i \tag{10.200}\cr \delta\psi^i &=& i\epsilon (\dot\phi^i-\Gamma^i_{jk}\overline\psi^j \psi^k)\tag{10.201}\cr \delta\overline\psi^i &=& -i\epsilon (\dot\phi^i-\Gamma^i_{jk}\overline\psi^j \psi^k). \tag{10.202}\end{eqnarray}$$
How can I quantise the classical supercharges
$$Q=i\overline\psi_i\dot\phi^i, \qquad \overline Q=-ig_{ij}\psi^i\dot\phi^j \tag{10.210}$$
in a way such that
$$ \delta F=[\epsilon Q+\overline\epsilon\overline{Q},F]_{\pm}$$
where $F$ is either a fermionic or bosonic field and $\pm$ is used appropriately?
The natural answer would be something like calculate conjugate momenta
$$ p_i=\frac{\partial L}{\partial\dot\phi^i}, \qquad \pi_{i\psi}=\frac{\partial L}{\partial\dot\psi^i}, \tag{10.207b}$$
and impose canonical commutation relations
$$ \begin{eqnarray} [\phi^i,p_j]&=&i\delta^i_j,\tag{10.208} \cr \{\psi^i,\pi_{\psi,j}\}&=&\delta^i_j.\tag{10.209}\end{eqnarray}$$
Since in doing this I face non-trivial ordering issues, which the book doesn't seem to be worried about, and moreover its quantized version of conjugate momentum to $\phi$ seems wrong to me, as well as its quantized $Q$ doesn't seem to reproduce the correct transformations for the fields, I ask if someone could clarify this.
Moreover, looking in the paper Constraints on supersymmetry breaking by Witten, in the neighbourhood of eqs. (90), (91), he seems to claim that the correct definition of conjugate momentum is derivative with respect to covariant derivative instead of time derivative, and this is another thing which leaves me with some doubts.
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Comment added: I should add that Vafa in the book at page 184 makes some comments about operator ordering, even though in a simpler case. The difference here is that, to my understanding, we have to provide an ordering (also in the susy transformations themselves) between $p_i,$ $\phi^j$ $\psi^k$ and $\overline\psi_m$ such that the obtained $Q$'s generate the transformations.