You could add the --no-merges
option to the hook here:
https://github.com/gera/gitzilla/blob/master/utils.py#L76
Change it to this:
asCommand = ['git', sCommand, "--no-merges",
"--format=format:%s%s" % (sSeparator, sFormatSpec)]
As this is a utility function, it may also be used by others checks (don't know), so take that into account when changing it.