Is there a natural way to deter flies?

You could make your own fly paper or purchase it. I haven't seen them used in years, but they are an alternative to spray. https://www.thespruce.com/how-to-make-fly-paper-1389064

Fly swatter! Vacuum cleaner hose! Fly paper!

Fly paper, I like the round tubes that hang from the ceiling.

or get one of those bug zappers that look like a tennis racket, or get an old fashioned fly swatter. If the flies are now the window, there is a clear sticky fly paper that you put on the window, and peel off when full.

Ziplock bags or glass containers filled with water will deter them. They fly up and see their reflection, enlarged in the water, and fly away.