The argument is not "bogus", it simply need to be qualified. Indeed, it is at the heart of the phenomena of (Landau) phase transitions, which is built on spontaneous symmetry breaking. You have a system that has some symmetry, yet we claim that it undergoes phase transition which breaks this symmetry - what gives?! In formal terms, we have an analytic expression for the partition function $Z = \sum \exp(-\beta E_n)$ yet we are looking for a non-analytical behavior which characterizes a phase transition.
The answer to these problems is indeed that the analytical nature of $Z$ holds only for finite sums. At the thermodynamic limit we can get non analytical behavior. In terms of symmetry, under ergodicity we assume that the system travels among all possible configurations with probability proportional to $\exp(-\beta E_n)$, but if we now set the magnetization going on one direction, it is clear that there is a huge energy barrier to flipping all the spins in the other direction. When taking the ergodic assumptions we said that averaging over systems is like averaging over long times, but it is clear that for the system to flip all the spins, the time scale is exponentially small in the energy barrier (for a low enough temperature). Even for not very large systems that may be much larger than the age of the universe! So we potentially solved both problems - however it is not yet clear how to address it analytically. As straight-forward averaging over quantities using $Z$ for finite system will still assume ergodicity and the symmetry would be manifest.
So there are two ways. In Monte-Carlo simulations, the system picks one magnetization when lowering the temperature. So each simulation by itself would actually give a finite magnetization that will persist over rather long cycles, at low temperatures. Averaging over different simulations might be problematic as different runs will pick different directions, randomly, so averaging over absolute value should solve that. But you can check that your simulation actually works when you lower the temperature and it randomly choose one magnetization and just sticks with it. It's fun!
A more formal way, which is also an analytical approach to phase transition, is to add a small symmetry-breaking term to the Hamiltonian, and then take a limit of large-system-small-term. So we write
$$H = J \sum \sigma_i \sigma_j - h \sum \sigma_i$$
and set $h$ to be very small. At the limit $N\to\infty$, $h\to 0$ such that $Nh\to \infty$, the phase transition will be evident. And again, this works even for not very large systems when doing averages using different numerical methods. For $T>T_c$ the effect of $h$ is small enough and the average magnetization is zero, while for $T<T_c$ the small term $h$ helps the system pick the right direction of magnetization, but the absolute value of the magnetization is not meaningfully affected by it. Again - you can try it at home.