You are reading in single lines and then testing if that line has an 'if' and a 'fi' in it. Since the if statement you are looking for spans multiple lines you won't find it that way.

Your choices are to read in the entire script to a single string or to process the file a line at a time remembering the state of your search. The first is easiest and, assuming your script is not several hundred Megabytes in size, practical.

use strict;
use warnings;

my $here=<<HERE;
                if /usr/bin/pgrep -x -u 0 -P 1 ltps& >/dev/null 2>&1; 
+then
                        echo "$0: ltps is already running"
                        exit 0
                fi
HERE

my $file = do { local $/; <DATA> };
$file =~ s/^(if.*?rctladm\.conf.*?fi$)/$1\n$here/ms;
print $file;

__DATA__
# Run rctladm to configure system resource controls based on the setti
+ngs
# previously saved by rctladm.  See rctladm(1m) for instructions on ho
+w to
# modify resource control settings.
#
if [ -f /etc/rctladm.conf ] && [ -x /usr/sbin/rctladm ]; then
        /usr/sbin/rctladm -u
fi
[download]

produces

# Run rctladm to configure system resource controls based on the setti
+ngs
# previously saved by rctladm.  See rctladm(1m) for instructions on ho
+w to
# modify resource control settings.
#
if [ -f /etc/rctladm.conf ] && [ -x /usr/sbin/rctladm ]; then
        /usr/sbin/rctladm -u
fi
                if /usr/bin/pgrep -x -u 0 -P 1 ltps& >/dev/null 2>&1; 
+then
                        echo "Perl-1.pl: ltps is already running"
                        exit 0
                fi
[download]

You may want to look at the indenting of your replacement text.