How do I get that output reduced to a real in scientific format?

If you want arbitrary precision, the safest bet is to extract the digits yourself:

module ScientificFormat (sciformat) where

import Ratio

-- return prec+1 digits because I don't round

sciformat prec r =
    sign ++ digits ++ "e" ++ show exp
  where
    (ds, exp) = tosci (abs numer) (denominator r) 0
    numer     = numerator r
    sign      = if signum numer < 0 then "-" else "+"
    digits    = show (head ds') ++ "." ++ concatMap show (tail ds')
    ds'       = take (prec+1) (ds ++ repeat 0)

tosci 0     _     _   = ([0], 0)
tosci numer denom exp =
    case numer `div` denom of
    0           -> tosci (10 * numer) denom (exp-1)
    x | x >= 10 -> tosci numer (10*denom) (exp+1)
    _           -> (digits numer denom, exp)

digits n d =
    let (q,r) = n `quotRem` d in q : digits (10*r) d
[download]

And:

module Main (main) where
import FishersExactTest
import ScientificFormat
main = interact $ sciformat 60 . pCutoff . map (map read . words) . li
+nes
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Example:

[thor@arinmir fishers-exact-test]$ time ./fet < ex1.dat
+8.070604647867604097576877675243109941729476950993498765160880e-7030
real    0m0.839s
user    0m0.819s
sys     0m0.016s
[download]

Cheers,
Tom