It's kinda weird to do this with top. Especially putting to a csv? This stuff is changing all the time- by default ordered by usage, likely- so just because something is not visible, does not mean a second later it didn't abuse your resources. Maybe ps aux might be of use here, to actually show you what's going on, compare output of that with same output a few mins later.. who knows.

What might be more useful is - what the heck are they trying to do? See what users are hogging resources?

If you want to monitor usage, cpu hit.. If a server is grinding to a hault.. etc .. Consider NAGIOS.

You can code plugins for nagios with perl to do more specific alerts for your org.

If you haven't a working nagios system, it would be in your best interest.
(Dunno. If you just want to do your 9-5... But there might be something off here. Coding to save top output to a db.. sounds like someone's not making the most of posix- like.. keeping a ferrari in second gear.)