Well, it think the problem is not with the "non-constantness". All $[m]$ are non-constant if $m \neq 0$. Silverman $(4.2a)$. The problem I see in your statement is that you need $[m]$ to be separable (not $\phi$).
Silverman Corollary 4.11:
Let $\phi:E_1 \rightarrow E_2$, $\psi:E_1 \rightarrow E_3$ be non-constant isogenies, and assume $\phi$ is separable. If $\text{Ker}(\phi) \subseteq \text{Ker}(\psi)$ then there exists a unique isogeny $\lambda$ s.t. $\psi = \lambda \circ \phi$.
In your case, $\phi(E_1[m]) = \mathcal{O}$ means that $E_1[m] = \text{Ker}([m])\subseteq \text{Ker}(\phi)$. Which is different from the theorem where the $\phi$ kernel is the subset and $\phi$ is separable.
$[m]$ is separable always if char$(K)=0$. If $K$ is a finite field of characteristic $p$ ($K$ is the field over which the isogenies/curves are defined) then by Silverman Corollary $5.5$ $[m]$ is separable if and only if $p$ does not divide $m$.
Therefore, if $[m]$ is separable, then by the theorem we get $\phi = \lambda \circ [m] = [m] \circ \lambda$ ($[m]$ "commutes" because $\lambda$ is an isogeny but technically those are different endomorphisms over diff. curves).
Not sure what to do if $p$ divides $m$. I guess then $\phi$ (separable) cannot be equal to $[m] \circ \lambda$ since $[m]$ is not separable.