Not sure if you figured this out on your own, but if you know how to remove a master plugin from a patch then you should be able to do it. While I personally haven't removed the crafting mods from my setup, I've removed a couple other ones and haven't seen an issue. If you remove CACO, you may want to look at a different mod that fixes the flora re-spawn bug. CACO had that built in.
If you haven't removed masters from a patch before, this is my favorite video on the steps you need to take. Fair warning, you will need to use Wrye Bash and that tool isn't covered by this guide. It's pretty straight forward though in this case.
Your other option is to not use the STEP patch and then you can use whatever mods you want, but you'd need to build your own CR patch and add other mods that handle the fixes the STEP patch does. Unless you are skipping most of the STEP mods, I'd suggest you keep the STEP patch and remove mods as necessary.
sirtechfan's post in Is it possible to skip the crafting overhauls? was marked as the answer