You're probably better off using piped open (see perlopentut) in this case, since that will give you the process id of the spawned process:

# set up alarm...
my $pid;
$SIG{ALRM} = sub { kill $pid; die "Timed out" };
alarm(5);
$pid = open PROG,"/some program|" or die "Can't fork: $!";
my $input = join('',<PROG>);
alarm(0);
close PROG;
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Note; code is untested.

update: added alarm() calls.