Separate eggs; cover both bowls with plastic wrap. Set aside at room temperature for 30 minutes. Toss shredded cheese with thyme; cover and set aside.
Preheat oven to 350 degrees F. In medium saucepan melt the 1/4 cup margarine or butter; stir in flour and pepper. Add milk. Cook and stir over medium heat just until thickened and bubbly. Remove from heat.
Add cheese mixture, a little at a time, stirring just until melted. In a medium mixing bowl beat egg yolks with a fork until smooth. Gradually stir cheese sauce into yolks. Set aside to cool (about 5 minutes).
Ina large mixing bowl beat egg whites until stiff peaks form (tips stand straight). Gently fold about half of the beaten egg whites into the cheese mixture to lighten it, then gently fold that mixture into remaining egg whites in the large bowl.
Pour into an ungreased 1-1/2-quart souffle dish. Bake for 40 minutes or until a knife inserted near center comes out clean.
Meanwhile, in a medium skillet heat the 1 tablespoon margarine or butter over medium heat. Cook pears and shallots, uncovered, for 4 to 5 minutes or until shallots are tender, stirring often. Add vinegar, honey, and salt; cook and stir 2 minutes more. Serve souffle immediately with pear mixture. Makes 6 main-dish servings.