Desde a versão 1.7.22, pngcrush
tem uma opção de substituição.
Tente
pngcrush -ow file.png
Veja Changelog para mais informações:
Version 1.7.22 (built with libpng-1.5.6 and zlib-1.2.5)
Added "-ow" (overwrite) option. The input file is overwritten and the
output file is just used temporarily and removed after it is copied
over the input file.. If you do not specify an output file, "pngout.png"
is used as the temporary file. Caution: the temporary file must be on
the same filesystem as the input file. Contributed by a group of students
of the University of Paris who were taking the "Understanding of Programs"
course and wished to gain familiarity with an open-source program.