Hey just asking, I collect those cron logs in a special mailbox (Google unlimited).
That does sound like a bad filter. I've got 24 filters with loads of conditions on my production box, and never encountered this. Almost all of my rules end execution though. Sounds like it's getting stuck in a loop continually reprocessing the rules over and over, that's bad. Also sounds like it's not passing something by reference. Reallocating memory all over the place, also bad. Can you screenshot the rules? I'd like to recreate it so we can make a proper bug report on github.
As for the email to department setup, I use that, but not in filters. I've added emails for each department and it knows that a message to sales@ gets put in the sales queue as that email address is set to that department, with their SLA and default priority etc. Can add as many emails as you like. Just disable fetching on them. (They all come from the same inbox, there's only one that actually fetches). I also have sending disabled on all, just using internal mail function to send.