Вы можете попробовать что-то вроде:
perl -pe 's/(\$\w+\[\s*)(?![A-Z\d]+\b)(\w+)(\s*])/$1\'$2\'$3/g' file.php
Пример:
echo $arr[foo] $arr['ok'] $arr[3] $arr[CAPS] $arr[$var] $arr[ bar ] | perl -pe "s/(\$\w+\[\s*)(?![A-Z\d]+\b)(\w+)(\s*])/$1'$2'$3/g"
$arr['foo'] $arr['ok'] $arr[3] $arr[CAPS] $arr[$var] $arr[ 'bar' ]