The following is a communal answer from the algebraic topology Discord [1], primarily put forward by Irakli Patchkoria (correcting previous half-answers by Tyler Lawson and me).
Kiran suggested it be recorded here to ease future reference.
The idea is to produce two topological realizations $M$, $N$ of a single $MU_*$–module by finding two distinct resolutions whose effect on homotopy is the same.
The two associated square-zero extensions then give a counterexample.
We'll reduce complexity first by considering $ku$–modules rather than $MU$–modules, and second by aiming for a $ku$–module whose homotopy cleaves into small even and odd parts, forcing its $ku_*$–module structure to trivialize.
$\DeclareMathOperator{\Sq}{Sq}
\newcommand{\F}{\mathbb{F}}
\newcommand{\Z}{\mathbb{Z}}
\newcommand{\HFtwo}{H\F_2}
\newcommand{\Susp}{\Sigma}
\newcommand{\co}{\colon\thinspace}$
The nice homotopy groups of complex $K$–theory, $ku_* = \Z[u]$, can be used to show that its bottom $k$–invariant $\kappa_{ku}$ is $ku$–linear: in the diagram
$$
\begin{array}{ccccc}
& & \Susp^4 ku \\
& & u \downarrow \\
\Susp^{-1} H\Z & \to & \Susp^2 ku & \to & \Susp^2 H\Z \\
& & u \downarrow \\
& & ku & \to & H\Z,
\end{array}
$$
the vertical maps are multiplication by homotopy elements, hence are $ku$–linear; in turn the horizontal co/fibers are also $ku$–linear; and, finally, the $k$–invariant appears as the middle composite, hence is also $ku$–linear.
Similarly, we can show the $ku$–linearity of the bottom $k$–invariant of $ku/2$ and of the Bockstein map $\beta\co \HFtwo \to \Susp H\Z$ (relying on the $ku$–linearity of $2\co H\Z \to H\Z$).
Stringing some of these together gives a $ku$–linear composite $$\HFtwo \xrightarrow{\kappa_{ku/2}} \Susp^3 \HFtwo \xrightarrow{\beta} \Susp^4 H\Z \to \Susp^4 \HFtwo.$$
The bottom $k$–invariant $\kappa_{ku/2}$ of $ku/2$ is given as the Milnor primitive $Q_1 = \Sq^3 + \Sq^2 \Sq^1$, the composite of the latter two maps is given as $\Sq^1$, and hence the whole composite is the nontrivial Steenrod operation $$\Sq^1 Q_1 = \Sq^1(\Sq^3 + \Sq^2 \Sq^1) = \Sq^3 \Sq^1.$$
Meanwhile, the homotopy groups of the cofiber $M$ of this composite are $\Susp \F_2 \oplus \Susp^4 \F_2$, which splits as a $ku_*$–module — hence this $ku_*$–module could alternatively be modeled by $N = \Susp H\F_2 \oplus \Susp^4 \HFtwo$ (i.e., the cofiber of the zero map).
To finish, set $E = ku \oplus M$ and $F = ku \oplus N$.