The -realclean target should use @rm -fr $(CONFIGS_DIR)/$(@:%-realclean=%)/piraha I think.
I would also suggest to add this to make.configuration whichsi where the actual work happens, not the wrapper Makefile in the Cactus root. Finally it may be better to make piraha a subdir of build (or scratch) which would automatically clean it in realclean (and clean).
One more (slightly unexpected, but actually perfectly correct) observed behaviour: I also found that once I remove the piraha directory and call make sim again, it does not trigger CST ie the piraha cache is not re-generated which may be ok (since the C code generated from the ccl files did not change). I guess that one would need a rebuild to force CST to re-run (after all the piraha files are just caches so need only be re-genreated when the ccl files change).