Is there a way to hide perl's command line from programs such as "ps"?

First of all note that if you're doing this for security reasons (to avoid people seeing passwords, for example) then you should rewrite your program so that critical information is never given as an argument. Hiding the arguments won't make your program completely secure.

To actually alter the visible command line, you can assign to the variable $0 as documented in the perlvar manpage. This won't work on all operating systems, though. Daemon programs like sendmail place their state there, as in: 

    $0 = "orcus [accepting connections]";