You can't brush in the NIK sharpening once you're back in Aperture, no. Basically Aperture hands a TIFF off to the NIK plugin and it gets an updated TIFF back. There's no way to selectively brush in parts of the new TIFF. That would be a good trick
While I love the NIK plugins, I tend to use them sparingly just because they break the "non-destructive" workflow of Aperture. And they give you the modified file which is usually about 6x the size of the original RAW file.