Welcome to GoY.
The thyme is attracting them. But only you can decide if you want to dig them out. Do the flies then come in the house? Do you find birds feeding on them? Are the thyme there for culinary use? Lots of things to consider before you decide.

You could always spread a bit of fine netting or fleece over them to keep the flies off. After all you wouldn't care for using any using herbs that bluebottles had tramped about on with their dirty feet.