The rule with fermions is as follows.
You get the momentum as a left-derivative of $L$; in other words, write $\dot{\psi}$ on the left of each factor so$$L=-\frac{i}{2}(\dot{\psi}\overline{\psi}+\dot{\overline{\psi}}\psi)\implies\Pi_\psi=-\frac{i}{2}\overline{\psi},\,\Pi_\overline{\psi}=-\frac{i}{2}\psi.$$
You get $H+L$ as a sum of $\dot{q}p$ terms, not $p\dot{q}$. So$$H=\dot{\psi}\Pi_\psi+\dot{\overline{\psi}}\Pi_\overline{\psi}-L=0.$$
Unfortunately, this example isn't very helpful pedagogically; $H=0$ doesn't happen in general. The problem here is (i) you only used time derivatives in $L$, not spacetime derivatives as expected in a field theory, & (ii) each term is proportional to a time derivative, so $L$ is just the value of $H+L$ from a Legendre transform. A more realistic $L$, assuming Cartesian spacetime coordinates in Minkowski space with the $+---$ convention, is$$L=-i\partial_\mu\psi\partial^\mu\overline{\psi}=i\partial_\mu\overline{\psi}\partial^\mu\psi\implies\Pi_\psi=-i\partial^0\overline{\psi},\,\Pi_\overline{\psi}=i\partial^0\psi\implies H=i\Pi_\overline{\Psi}\Pi_\Psi+i\partial_j\psi\partial^j\overline{\psi}.$$Note that, unlike in discrete mechanics, a field theory's Hamiltonian depends on not just canonical fields and conjugate momentum densities, but also space (but not time) derivatives of canonical fields. Meanwhile, because the Legendre transform introduces two $\dot{q}p$ terms but $-L$ only cancels one of them, I've kept one, which has had its $\dot{q}$ factor rewritten in terms of $p$s (you always have to do that when obtaining $H$, although sometimes $\partial_jq$ is also needed to do it).
You get Hamilton's equations with right-derivatives of $H$. For example, $\dot{\psi}=i\Pi_\overline{\Psi}$, but to obtain $\dot{\overline{\Psi}}$ by differentiating $H$ with respect to $\Pi_\overline{\Psi}$ the two-momenta term must be rewritten with that momentum on the write, which as expected gives an extra $-$ sign. Note these results match what $L$ gave us.