Put more light on the leggy plants. Wind doesn't make a plant leggy unless the wind is strong enough to blow away the light .
You can't prune those seedlings. There is nothing to prune. Maybe I misinterpreted what you meant.
You can bury the stems after a transplant but from what I see in the pictures, I wouldn't worry about it too much at this point. If you keep a breeze blowing on the plants they will get stronger... if given more light.
- Ares Schizas likes this