You will not be able to do this kind of selection (lasso) directly in Indesign. You can do a number of things. If the background map is not too involved, you could apply a multiply effect to the PDF of handwritten text. If that doesn't work, you could open or extract the image into Photoshop. Then convert to a bitmap image, and place and colorize new image in Indesign.
Place the PDF and make sure to check the show options box. Choose transparent background (this may or may not be grayed out depending on how the PDF was created).