There are many countermeasures that can be done, we've only implemented a subset of them as more haven't been needed.
Mainly we wait some time to make sure any conflicting transaction has time to propagate on the network. We have well connected nodes with basic redundancy.
When they are available we sometimes use external block explorers for certain nice-to-have enhancements, but it's absolutely not required for zeroconf as they are frequently down.
I can of course only speak to our custom-built setup, presumably everyone who accepts payments with bitcoin uses something similar. Regardless, let's maybe not go as far as to say that anyone who accepts payments with bitcoin is attacking bitcoin ;)