It's a big ocean. Most of the species aren't spending significant time in the runoff anyway. I have seen runoff muddy the water to the point the fishing sucks especially at 2nd Ave Pier, but it's not from the bacteria. It's not like this is a new development. Wither's Swash is known for being disgusting.
Cook your fish until done, and you should be fine. I doubt there is much testing that can be done by DHEC anyway.
For those who haven't seen there is a long term swimming advisory due to bacteria levels along almost all of Myrtle Beach and most of Surfside.