You can look at the ipk's table of contents and manually rm those files. ipks are just tar files, so to find the table of contents for (e.g.) foo.ipk, you
tar tvf foo.ipk
Some ipks have just three files inside, one of which is the tar file you want. Suppose it's bar.tar.gz. Then to see what's inside you can try something like
tar xOf foo.ipk bar.tar.gz | tar tzvf -