Heat a large saute pan over medium-high heat. Add the olive oil and the garlic cloves and cook for 3 to 4 minutes, to flavor the oil. Carefully remove the garlic using a slotted spoon, and reserve. Add the broccoli rabe to the pan in batches; it will crowd the pan at first but will wilt quickly. Season with salt and pepper. Slice the reserved garlic.
When the broccoli rabe has wilted, about 3 minutes, add the shallot, the sliced garlic, and the pepper flakes. Continue cooking until the shallot has softened and the broccoli rabe is cooked through but still has some bite, another 2 minutes. Serve with a squeeze of lemon.