Maybe you can just run the substitution and limit it by time and/or number of replacements?
Here's a quick'n dirty example:

use strict;
use warnings;


{
  my $count;
  my $timeout;

  sub set_count   { $count   = shift; }
  sub set_timeout { $timeout = $_[0] ? time() + $_[0] : 0; }

  sub limited_subst {
    my ($from, $replacement) = @_;

    die "Too many replacements!" unless $count--;
    die "Time is up!"            if $timeout and time() > $timeout;
    sleep(1); # just for demonstration!
#    warn "Replacing $from -> $replacement\n";
    return $replacement;
  }
}


sub test_replace {
  my ($string, $from, $replacement, $limit, $timeout_epoch)   = @_;
  my $rollback = $string;

  set_count(   $limit );
  set_timeout( $timeout_epoch );

  eval {
    $string =~ s/ ($from) / limited_subst($1, $replacement ) /gxe;
  };

  if ($@) {
    print "Oops! $@";
    $string = $rollback;
  }

  return $string;
}


my $string      = "la " x 30;

print "Checking with no real limit:\n";
print "in : $string\nout: ", test_replace($string, 'la', 'ho!', -1, 0)
+, "\n\n";

print "Checking with subst_limit 3:\n";
print "in : $string\nout: ", test_replace($string, 'la', 'ho!', 3,  0)
+, "\n\n";

print "Checking with timeout 3:\n";
print "in : $string\nout :", test_replace($string, 'la', 'ho!', 30000,
+ 3), "\n\n";


__END__
Output:

Checking with no real limit:
in : la la la la la la la la la la la la la la la la la la la la la la
+ la la la la la la la la
out: ho! ho! ho! ho! ho! ho! ho! ho! ho! ho! ho! ho! ho! ho! ho! ho! h
+o! ho! ho! ho! ho! ho! ho! ho! ho! ho! ho! ho! ho! ho!

Checking with subst_limit 3:
Oops! Too many replacements! at 910736.pl line 15.
in : la la la la la la la la la la la la la la la la la la la la la la
+ la la la la la la la la
out: la la la la la la la la la la la la la la la la la la la la la la
+ la la la la la la la la

Checking with timeout 3:
Oops! Time is up! at 910736.pl line 16.
in : la la la la la la la la la la la la la la la la la la la la la la
+ la la la la la la la la
out :la la la la la la la la la la la la la la la la la la la la la la
+ la la la la la la la la
[download]

Another idea: Maybe, you can start a sub-process that operates in a limited shell?
Important: I didn't scrutinized this for security holes!