Making tomato mix thicker without surge in calories
Your primary option if you want to add a thickener, you can use any hydrocolloid you wish. I will not list them here again, since it isn't necessary that every single question on thickeners on the site gets the full list. You can download Martin Lersch's free reference book, Texture: a hydrocolloid recipe book, and start experimenting. I can also not tell you which one will be the best for your case - they all produce different textures, and it depends on your personal preference which one to use, and anyway, you have to see which one is accessible for you.
A second option for getting any tomato based liquid thicker is to either cook it down on your own, or to replace some of the fresh tomatoes by concentrated tomato paste.
The third option, deseeding, was already given in Keith Ford's answer.
And you already mentioned the fourth, bulking up with dry ingredients such as your soy powder.
I would say the four together give you a pretty wide range of alternatives, try them out and see which one you can best live with.