This is the combination of japhy's solution with mine reposted here for completeness:

my (@prefixs, @suffixs);

for (@exclusions) {
  my ($p, $s) = split /ALPHA/, $_, 2;
  push @prefixs, $p;
  push @suffixs, $s;
}

$total_raw =
    "(?!" .  # Negative Lookahead: Any exceptional ALPHA

        "(" .
          join ("|", # Form (a|b|c) out of exceptional ALPHAs

              map ( # Form each exceptional ALPHA i

                  # Lookbehind for prefix i
                  "(?<=\Q$prefixs[$_]\E)" .

                  "ALPHA" .

                  # Lookahead for suffix i
                  "(?=\Q$suffixs[$_]\E)",

                  # where i = 0 to number of exceptions
                  (0..$#exclusions)
              )
          ) .
        ")" .
    ")" .

    .
    # Then match an ALPHA normally.
    # (We have already looked ahead and
    # confirmed that it is not exceptional)

    "ALPHA";

$total_rx = qr/$total_raw/;
[download]

$total_rx will only match a non-exceptional ALPHA, without modifying the string your searching on, and it doesn't forget any weird cases. It is a thing of beauty. :)

Enjoy,

-Andrew.