Can I lay stepping stones over a french drain?
Admittedly guesswork, but...

I would expect that, over time, the flagstones would settle into the gravel and mostly stabilize themselves (outside of frost heave and similar issues). There still could be tripping hazards, though, just as there can be with bricks after frost heave and tree roots lift them...  

Note that the french drain doesn't have to be exposed through the full 360-degree circuit of the house. If there's a short section where you have a walkway, that probably won't make much practical difference, as long as the whole thing is able to drain properly.