This would make it a lot easier to deploy sites and unzip the jquery cycle library into it's own dir instead of one that already exists. [At least for my use case when using drush make it would :) .] It looks like this would only be a minor patch to do this although I appreciate that this is probably also affects the 6.x-3.0-dev branch. If you are amenable to this suggestions perhaps the same could be done for the json2 library on github.
Here are two patches, one for each library.