Rather than trying to keep track of indices, it probably makes more sense to just use a hash. Something with logic similar to:

#!/usr/bin/perl -w
use strict;

my @records = <DATA>;
my @AoA = map [split /\s*\|\s*/], @records;

my %SPUsers = map {$_=>1} ("bill", "mike", "kevin", "mmartin", "sp");

my %excluded;
for my $row (@AoA) {
    if ($SPUsers{$row->[1]}) {
        $excluded{$row}++;
    }
}

for my $row (@AoA) {
    next if $excluded{$row};
    print join "|", @$row;
}

__DATA__
922337219576856 |rgiles   |5005444 |156 |pts/220 |9:00:44
922337219576856 |mrandall |3309650 |35  |none    |9:10:44
922337219576856 |mmartin  |4565899 |122 |pts/101 |9:15:44
59761456123786  |rkelly   |5555555 |999 |pts/900 |9:00:00
59761456123786  |mvick    |1234567 |886 |none    |9:20:00
59761456123786  |jrussel  |7654321 |456 |tty/101 |10:00:00
86555522211     |cklien   |5151515 |000 |tty/100 |10:00:00
86555522211     |mmartin  |1234567 |987 |none    |11:00:00
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