I don't know what other people think, but I did exactly what you suggest somewhere in my Chemistry::Mol module. From the POD:

$mol->sort_atoms($sub_ref)

Sort the atoms in the molecule by using the comparison function given in $sub_ref. This function should take two atoms as parameters and return -1, 0, or 1 depending on whether the first atom should go first, same, or after the second atom. For example, to sort by atomic number, you could use the following:

$mol->sort( sub { $_[0]->Z <=> $_[1]->Z } );

Note that the atoms are passed as parameters and not as the package variables $a and $b like the core sort function does. This is because $mol->sort will likely be called from another package and we don't want to play with another package's symbol table.