.diff.gz became as big as upstream source

[GCS <gcs@lsc.hu>]

Hi,

 I have a small package, which generates configure, Makefile[.in] at
every compilation. As upstream already contained these files, when I
build my package, and these files are regenerated but different versions
of auto[conf|make], I get a big .diff.gz (as big as upstream source).
Policy says I should not tamper with upstream source except where really
necessary; but am I allowed to delete these files from upstream,
generate them from debian/rules and clean again afterwards? It would
make the .diff.gz very small, without any differences in .deb .

Cheers,
Laszlo/GCS