In a pot, add butter and saute onion and garlic, until softened. Transfer the onion and garlic to a blender, along with the tomatoes. Puree until smooth.
Add tomato mixture, chicken stock, and thyme into the pot. Bring to a simmer, cover, and cook for 10 minutes.
Meanwhile, make the grilled cheese croutons: assemble sandwiches by placing 2 slices of cheese and 2-3 slices of bacon in between 2 slices of bread. Heat butter in a pan and brown sandwiches until the cheese has melted and the bread is toasted. Set aside to slightly cool.
Slice into crouton cubes.
To serve, ladle soup into bowls and place grilled cheese croutons on top.