I think, I have found a work around for this. After looking at here I found that SQL::Tokenizer was suitable for my case and used regex used by the Tokenizer module to sanitize my query. It needs a little working on but, for now works for most of my test cases.

use strict;
my $insane_sql = shift or die "usage sanitize_sql_query.pl <insane que
+ry>";
print "\n\n$insane_sql\n\n";
my $sane_sql = "";

#Match anything inside single quotes. 
#Got it from SQL::Tokenizer.
#Author:Igor Sutton Lopes
while ($insane_sql =~ m/'.*?(?:(?:''){1,}'|(?<!['\\])'(?!')|\\'{2})/sm
+xg) 
{
    my $pre_match = $`;
    my $match = $&;
    my $post_match = $';
    print "Match: $match\n";
    $match =~ s/'//g; #replace the single quotes
    $match =~ s/\W/_/g; #sanitize the match
    $insane_sql = $pre_match . $match . $post_match;
}
print "\n\n$insane_sql\n\n";

__END__
perl sanitize_sql_query.pl "SELECT TO_DATE(['(PDH-CSV 4.0) (Central St
+andard Time)(360)']) AS CAPTUREDATE, AVG(TO_REAL(['\\Server\LogicalDi
+sk(N:)\Avg. Disk sec/Read'])) AS AVG_LOG_SEC_READ FROM 'C:\PerfCSV\Se
+rver_01200549.csv' GROUP BY TO_DATE(['(PDH-CSV 4.0) (Central Standard
+ Time)(360)'])"

SELECT TO_DATE(['(PDH-CSV 4.0) (Central Standard Time)(360)']) AS CAPT
+UREDATE, AVG(TO_REAL(['\\Server\LogicalDisk(N:)\Avg. Disk sec/Read'])
+) AS AVG_LOG_SEC_READ FROM 'C:\PerfCSV\Server_01200549.csv' GROUP BY 
+TO_DATE(['(PDH-CSV 4.0) (Central Standard Time)(360)'])

Match: '(PDH-CSV 4.0) (Central Standard Time)(360)'
Match: '\\Server\LogicalDisk(N:)\Avg. Disk sec/Read'
Match: 'C:\PerfCSV\Server_01200549.csv'
Match: '(PDH-CSV 4.0) (Central Standard Time)(360)'

SELECT TO_DATE([_PDH_CSV_4_0_Central_Standard_Time_360_]) AS CAPTUREDA
+TE, AVG(TO_REAL([_Server_LogicalDisk_N_Avg_Disk_sec_Read])) AS AVG_LO
+G_SEC_READFROM C_PerfCSV_Server_01200549_csv GROUP BY TO_DATE([_PDH_C
+SV_4_0_Central_Standard_Time_360_])
[download]

Edit: $match =~ s/\W+/_/g;, this should have actually been $match =~ s/\W/_/g; since we need all special characters to be converted to an underscore.