This is a bit simpler than yours, a lot simpler than the CPAN 'solutions', and it works even if the program produces a lot of output:

#! perl -slw
use strict;
use IPC::Open3;
use threads stack_size => 4096;

## Kill 0,pid does appear to work properly,
## It return true even after the executable is dead & gone
sub checkPid{
    scalar( `tasklist /nh /fi "pid eq $_[0]"` !~ m[INFO]sm );
}

sub execute {
    my(  $timeout, @command, ) = @_;
    my( $err, $in, $out ) = do{ local *FH; \*FH };
    my $pid = open3( $in, $out, $err, @command )
        or die "@command : $!/$@/$^E";
    my( $Tout ) = threads->create( sub{
        my( $Terr ) = threads->create( sub{ my @in = <$err>; return \@
+in } );
        my @in = <$out>;
        return \@in, $Terr->join;
    } );
    sleep 1 while checkPid( $pid ) and --$timeout;
    kill 3, $pid unless $timeout;
    return $Tout->join, $timeout == 0;
}

my @cmd = (
    'perl.exe',
    q[-le"$|++; print($_), warn( $_), Win32::Sleep 250 for 1 .. 12" ]
);
my( $out, $err, $timeout ) = execute( 2, @cmd );

print 'Command ', $timeout ? 'timed out' : 'completed';
print "From stdout:[\n @$out ]" if @$out;
print "From stderr:[\n @$err ]\n" if @$err;

( $out, $err, $timeout ) = execute( 5, @cmd );
print 'Command ', $timeout ? 'timed out' : 'completed';
print "From stdout:[\n @$out ]" if @$out;
print "From stderr:[\n @$err ]" if @$err;
[download]

Produces:

C:\test>869942
Command timed out
From stdout:[
 1
 2
 3
 4
 5
 ]
From stderr:[
 1 at -e line 1.
 2 at -e line 1.
 3 at -e line 1.
 4 at -e line 1.
 5 at -e line 1.
 ]

Command completed
From stdout:[
 1
 2
 3
 4
 5
 6
 7
 8
 9
 10
 11
 12
 ]
From stderr:[
 1 at -e line 1.
 2 at -e line 1.
 3 at -e line 1.
 4 at -e line 1.
 5 at -e line 1.
 6 at -e line 1.
 7 at -e line 1.
 8 at -e line 1.
 9 at -e line 1.
 10 at -e line 1.
 11 at -e line 1.
 12 at -e line 1.
 ]
[download]

The discrepancy between the 1 1/4 seconds of output gathered and the 2 second timeout in the first run, is down to pipe buffering.