Yes you can. The difference is that your cookies will now be stuffed with plain peanut butter and not the chocolate version. The other difference is the change in the consistency of your cookie centers - it will now be a lot softer. You can add more icing sugar to compensate for the cocoa powder but that might make your stuffed cookie centers too sweet. The other way is to chill or freeze the peanut butter filling thoroughly so that it is easier to work with.