If you're using the XML output for BLAST, the following XSLT stylesheet only prints the first hit.

usage:

    xsltproc --novalid firsthit.xsl blast.xml

Of course, you can easily modify the rule 'select="Hit[1]""' to match your needs. eg.

    select="Hit[number(Hsp_score)>100]"

I don't think there is an option to blastall/rpsblast which will fix this issue. This usage guide states, for the -b flag, that "This is not the number of alignment segments or HSPs, since a given domain may have more than one portion aligned to the query."

You could get a list with only the top hit, ignoring the composite HSPs, by parsing the BLAST output. Using the SearchIO library from Bioperl, something like this should work:

#!/usr/bin/perl -w

use strict;
use Bio::SearchIO;
my $searchio = Bio::SearchIO->new(-file => "myblastfile", -format => "blast");

while(my $result = $searchio->next_result) {
  while(my $hit = $result->next_hit) {
    my @output = ($result->query_name, $hit->name, $hit->raw_score,
                  $hit->bits, $hit->significance);
    print join("\t", @output), "\n";
  }
}

This is just an example with some selected BLAST statistics (raw score, bit score etc.); see the documentation for how to access other parts of the BLAST report.

If you want to reduce redundancy of your hits, you may pre-process your target database using CD-HIT. For example you may use a threshold (say 40%, so that no 2 sequences in your dataset will be of more than 40% similar). Depending up on your need you may use a stringent threshold (<=40%) or lenient (>=40%). For the statistical detail of the CD-HIT algorithm you may refer to the following papers (1, 2 and 3)