If you know you'll be running on a linux system you could look at getrlimit(2) and setrlimit(2). Assuming that syscall.ph has been correctly h2ph'd you should be able to get this to work from within perl. All you'd need to do then is to set your RLIMIT_CPU to, say, 1 second and your script will be killed by the kernel if it uses more than that.

The advantage is that it's dependent on how much CPU time your script uses. If the server is busy with some other process your script may run for a lot of wall-clock time, but it will not be killed prematurely.

The same functionality no doubt exists in other systems, but this is not going to be the most portable implementation in the world.

We used this to good effect within the suexec wrapper for Apache - at the same time you can prevent memory hogs and fork() bombs, and it applies to all CGI scripts on the server.