How do I export goods if there's a factory consuming them?

Well I don't know how I would prove that it was the raw resource not the processed resource being exported if I tried to outpace the factory, so I'll just suggest the most obvious solution.

Shut down the factory. It may be painful, but you should be able to shift income to other exports for a while.

As you can see, the factory has produced nothing in at least 1 year, and I'm still successfully exporting Tobacco. $11,822 worth, to be exact.

To export pineapple create a cannery next to the pineapple farms as well as build a teamstars office next to the cannery.

you can fire all of the workers in the factory which spends the resources you want to export