I looked at cgi-bin. There are two files, php and php5, each 8 MB in size. That seems a bit odd. But in this small site, we're not using php, so we're OK.
I realized the script we are running is not invoked by apache. It's run by chron and that invokes the .pl file (it's a log file aggregator). So although I removed the ScriptAlias, the script still runs.
I have a few more questions, but they are more complex, so I'll wait till later to pose them. Thanks for your help so far.