One can obtain a little more in Geoff's situation, where $O_p(G) > 1$. Write $U = O_p(G)$ and $U_i = U \cap H_i$, so $U_i = O_p(H_i)$, as Geoff showed. In particular, $|U_1| = |U_2|$. Note that the $U_i$ are proper in $U$. I claim that $U = U_1U_2$.
First, observe that $U_1 \triangleleft G$ since $N_H(U_1)$ contains $H_1$ properly because $N_U(U_1) > U_1$. Since $H_1$ is maximal, $U_1 \triangleleft G$, as claimed. Next, $U/U_1$ is $G$-chief by the maximality of $H_1$, and in particular, $U/U_1$ is abelian. Since $G = UH_2$, it follows that $H_2$ acts irreducibly on $U/U_1$. Now $H_2$ normalizes $U_2$, so it normalizes $U_1U_2$. Since $U_1 \subseteq U_1U_2 \subseteq U$, we have either $U_1U_2 = U_1$ or $U_1U_2 = U$.
Since $|U_1| = |U_2|$, the first possibility yields $U_1 = U_2$, and this is a normal subgroup invariant under an isomorphism from $H_1$ to $H_2$, so we have that the $U_i$ are trivial in this case, and $U$ is minimal normal in $G$. Since $G = UH_2$, this implies that $H_2$ is maximal, contrary to assumption. We thus have $U_1U_2 = U$, as claimed. In particular, this yields $G = H_1H_2$.
But where do we go from there?
OK, now I know where to go. I can finish the proof in the case where $O_p(G)$ is nontrivial.
Assume $G$ is a minimal counterexample. Let $D_2 = H_1 \cap H_2$ and let $D_1$ be the image of $D_2$ under some isomorphism from $H_2$ onto $H_1$. Thus $D_1$ and $D_2$ are isomorphic subgroups of $H_1$ with $p$-power index equal to $|G:H_2|$. I claim that $D_1$ is maximal in $H_1$ but $D_2$ is not, and also $O_p(H_1) = U_1 > 1$. Since $G$ is a minimal counterexample and $H_1 < G$, this will be contradict the minimality of $G$.
First, to see that $D_2$ is not maximal in $H_1$, choose a subgroup $X$ with $H_2 < X < G$. Since $H_1H_2 = G$, we deduce that $D_2 = H_1 \cap H_2 < H_1 \cap X < H_1$, as wanted.
Next, to show that $D_1$ is maximal in $H_1$, it suffices via the isomorphism to show that $D_2$ is maximal in $H_2$. Note that $H_1 = U_1D_2$ by Dedekind's lemma. Suppose $D_2 < Y < H_2$. Recall that $U_1 \triangleleft G$, so $H_1Y = U_1D_2Y = U_1Y$ is a subgroup. Also, $|H_1Y:H_1| = |Y:D_2|$, and it follows that $H_1 < H_1Y < G$, contradicting the maximality of $H_1$.
Now we need a proof (or counterexample) in the case where $O_p(G) = 1$.