Suppose $P\in E(\mathbb{F}_q)$ and $R=dP$.
In the MOV attack, we compute $\alpha=e(P,T)$ and $\beta=e(R,T)$ and try to solve the discrete logarithm problem for $\alpha$ and $\beta$ in the finite field $\mathbb{F}_{q^k}$ where $k$ is the embedding degree.
But if $E(\mathbb{F}_q)$ is cyclic (which it can be even in the supersingular case), $\alpha,\beta$ are doomed to be $1$.
So what am I missing here?