A workaround would be to not use the blocking function of join. Something like this would work:

#!/usr/bin/env perl

use strict;
use warnings;
use threads;

sub worker {
    print "Worker thread started.\n";
    while(1){}
}

my $thread = threads->create(\&worker);

print "Setting alarm.\n";
$SIG{ALRM} = sub { die "Alarm!\n" };
alarm 2;

print "Check join\n";
while (threads::running) {
    $_->join for threads->list(threads::joinable);
}
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Yes, I am aware that this will spin like crazy, wasting a lot of system resources, however you can't sleep to limit this, as sleep is sometimes implemented using the system alarm. Actually thinking about it some more, I suspect that join may have been modified to use the system alarm, hence wiping out the alarm you initially set, causing it to never trigger.

Based on this, a "better" approach could be something like this:

#!/usr/bin/env perl

use strict;
use warnings;
use threads;

use constant TIMEOUT => 2;

sub worker {
    print "Worker thread started.\n";
    while(1){}
}

my $thread = threads->create(\&worker);

print "Check join\n";
while (1) {
    $_->join for threads->list(threads::joinable);

    last unless threads->list(threads::running);
    die "Alarm!\n" if time - $^T > TIMEOUT;

    select(undef,undef,undef,0.5);
}
[download]

Update: Updated second code example