Here's the methodology: We first write out the equation of motion for $\phi(x,t)$ in the Heisenberg picture. This is identical to classical field equation. Now, we solve the equations perturbatively, pretending that we're perturbatively solving the interacting Euler Lagrange equations from classical field theory. This perturbation series will involve only tree diagrams.
After we have the perturbation series, we can re-interpret $a_p$ and $a^{\dagger}_p$ appearing in the series as operators satisfying $[a, a^{\dagger}]=\delta$. The correspondence between Poisson brackets and commutators guarantees that we can re-interpret the variables as operators.
After we have the full $\phi(x,t)$ solution in the interacting theory, we can plug it into the LSZ formula to get interaction amplitudes.
This method is computationally complicated, which is probably why we use the full interaction picture for QFT. But nevertheless, doesn't it show that QFT involves only tree diagrams identical to CFT, provided that we work in the Heisenberg picture? Or is it possible that this method is wrong?