That could work, but it'd give you a pretty poor response time since your commands wouldn't be executed until the Arduino polled the database.
Can you connect the Arduino USB to the host that the web app is running on? If so, you could use a serial command interface and have the webapp send commands to the Arduino whenever it needed the Arduino to do anything. You can still use the database locally within the webapp to persist the current state and have it go back to that state if the webapp gets reset for any reason. This approach is simple to implement and also simple to test.
If a USB interface isn't available but your Arduino has a network interface then the next simplest approach would be to have the Arduino implement a web server which accepts HTTP requests containing commands. This would be equivalent to a conventional web service rather than a web app, in other words the Arduino would just expect HTTP requests containing commands to do something, rather than being asked to serve out the user interface too. With this approach the web app would act as a web server for the user interface, but the implementation would execute HTTP requests to the Arduino commanding it to do things - conceptually very similar to the serial approach but using HTTP as the communication mechanism.