The transmission rate of a low-energy Ar^q+ ion beam through a macroscopic glass tube of large aspect ratio is simulated. Secondary electron (SE) emission, induced by ion impacts with the inner surface of the capillary, are taken explicitly into account by adding a SE source term to the charge dynamics equation. We find that the additional SE channel significantly alters the distribution of the deposited charge in the capillary wall. Compared to the case without the SE channel, the electric field generated by the self-organized charge patches is generally weaker, yielding drastically different transmission rates, especially for higher beam intensities. The effect of SEs on the patch formation and resulting transmission rate is found to be significant for SE yields as low as 1 SE per ion impact, in the case of Ar+ ions. We propose a numerical experiment that can be tested experimentally, potentially allowing us to conclude if the SE channel is indeed crucial for accurately simulating the guiding of an ion beam through insulating capillaries. In the long run, our simulations may provide theoretical support for measuring the SE yield of low-energy ions impacting insulating surfaces at grazing angles.