"infected the pfsense server since it is part of the network as well."
Via what service?? What virus/worm are you aware of that can infect freebsd via what service? Pfsense only listens on a couple ports. Say ntp, ssh, http(s) what other applications are running and listening on the network that some sort of worm could exploit and infect freebsd?
If you are seeing some sort of flag from your ips that something is bad - then investigate where its coming from. You have not shown this traffic is coming from pfsense itself, nor have you even validated that its not some false positive..
I agree you should investigate such traffic - but jumping to think that something infected pfsense vs looking to what else it might be is jumping the gun a bit..