I had a similar hack on a site running Vbulletin 3 with a sneaky js redirect insert.
This is the shell script I used
Code:
for i in $(find . -name '*.php')
do
sed -i -r 's#eval\(base64_decode\([^\)]+\)\);##g' "${i}"
done
Only good if the code inserted starts with eval(base64_decode(.
That's just a temporary fix, though.