"I want my users to use the ordering plugin to change the order of my sobi listings. However I've just read that I need to turn the sobi seconde cache off. I cannot do this as I need the second cache on for another component I have."

For the order of search results you can keep the cache on, but, regarding the sobi2 cache system, the frontend listing is saved in the cache. The plugin allow each user to change the front end. Then is not possible to save the cache on the server each time a user change the sorting. That make sense.

But, If you (the admin) set a fixed sorting value in the backend, and dont let the user to change the sorting, then you can let the cache on. Because the cache is deleted each time an entry is added.