Combine flour, thyme, salt, and pepper on plate. Coat cod in flour mixture.
In a medium nonstick skillet, melt 2 tablespoons of yogurt spread over medium-high heat and cook the cod, turning once until fish flakes, about 8 minutes.
Meanwhile, in a large nonstick skillet, melt remaining spread over medium-high heat and cook the green beans, onion, and peas until tender, stirring occasionally, about 8 minutes. Add remaining ingredients and toss.