No shell C, você poderia fazer algo assim:
foreach i ( 'find -name "*.php"' )
sed '/^eval(base64_decode("DQplcnJvcl9yZXBvcnR"));$/d' $i > $i.new
mv $i.new $i
end
No bash, ficaria assim:
for i in $(find -name "*.php"); do
sed '/^eval(base64_decode("DQplcnJvcl9yZXBvcnR"));$/d' $i > $i.new
mv $i.new $i
done