Combine water and salt in a heavy saucepan. Add rice and cook according to package directions; drain and set aside.
Fry bacon; crumble and set aside, reserving 2 tablespoons drippings. Sauté onions in bacon drippings until soft.
In a 11/2-quart casserole dish, combine the cooked rice, bacon, onions, tomatoes, thyme, and cheese; mix well. Cover and bake at 350º for 25 minutes.