Prepare sauce while pasta is cooking: Heat olive oil and cook bacon until golden, 3 to 4 minutes. Stir in shallots, garlic and thyme, cook for 1 additional minute. Make roux by whisking in flour and cook an additional 3minutes, whisking constantly. Gradually add half and half, whisking constantly and bring just to a boil. Reduce heat, stirring occasionally, and simmer until, thickened, about five more minutes. Add salt, pepper and remaining cheese. Stir until cheese melts. Remove from heat and combine with pasta and basil.