I don't have experience with alarm(), and given that "Use them at your own risk" quote, I don't think I'm going to investigate it either. What I do have experience with, is processing long-running jobs. The general approach I use is to have the web interface kick off a batch job, which runs separate from Apache.

I happen to use a POE daemon, and track batch jobs through a table in MySQL. The web interface polls this table at regular intervals, and displays the progress (or the end-result) to the user. The POE daemon can process many jobs concurrently (through POE::Component::JobQueue and POE::Wheel::Run).

The advantage of that approach is that both sides are decoupled, and that you have detailed control over the resource consumption.

Update: Maybe you could make use of Apache2::SubProcess. That looks like a safe way to fork under mod_perl.