Yes, you can use
latexmk -C (or
-c) just to clean up auxiliary files. By default,
-c cleans up the following files types:
@generated_exts = ( 'aux', 'bcf', 'fls', 'idx', 'ind', 'lof', 'lot',
'out', 'toc' );
latexmk.pl, l. 1088f)
-C also cleans up the actual output, i.e pdf, dvi, or what have you. If you want to add more file extensions to this list, have a look at http://tex.stackexchange.com/a/83386/4012.
latexmk -C /
-c can be run no matter how you initially compiled your document, and may very well be used only for cleanup.