Basically, that's what I would do.
I found it useful to ask myself why I am doing something before I do it. When you say you will prune the side branches, the question is why are doing that? What goal does pruning these branches next season accomplish in terms of developing your bonsai? If you can't answer the question, best not to do it. If your single aim is fattening the trunk, why cut anything until you are happy with the thickness? If all I was trying to do right now is fatten the trunk, I would let it grow wild and not cut anything.
But this is not the only way. Allowing the trunk to fatten up to 2" and then cutting it will leave a large scar that will take years to heal (if it heals). If the trunk doesn't have lower movement, an alternative way to proceed would be to cut lower down sooner rather than later and allow the tree to backbud and grow a new leader. The tree would be allowed to grow from there or even grown and cut each season or so. This will give you smaller wounds and more movement, although it will take longer to obtained the desired thickness.
There are no perfect solutions in bonsai. There is a cause and effect to our actions, however, and we can choose our path once we under the relationship.