You already said that the performance of the application is irrelevant in this case, so it comes down to the cost of development and maintenance.

From the sound of it, it seems that while the OP realizes this, his PHBs may care deeply about performance. Perl is at a natural disadvantage in this case, since it sounds like their running a persistant environment for Java, but not for Perl.

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I wanted to explore how Perl's closures can be manipulated, and ended up creating an object system by accident.
-- Schemer

Note: All code is untested, unless otherwise stated

Actually, I suspect Perl will mop the floor with Java in this case, unless someone goes to great lengths to use the new direct io classes in the latest Java release. This is not a case where a small script is being launched over and over (which would favor a persistent environment over CGI), but rather a very heavy script that is run infrequently. In that situation, the actual file-processing speed is much more important than the startup time.