This kind of strategy is just sad, telling from the perspective of an SEO.
I came up with a nice oneliner to clear all that nasty code. Works great for me. May be useful for others.
find . -name "*.php" -print0 | \
xargs -0 -n 1 grep -l -Z eval.*base64 | \
xargs -0 -n 1 sed -i'.old' '/eval.*base64/ d'