I think that Any program like Peerguardian would still show up as trying to interfere with SC2 code and would still result in a ban or something, either that or the game would refuse to run.
Small firewall programs will not appear as interfering. If Blizzard receives anything it would be a connection timeout error. Just like if your internet went down while playing.
I have been using Peer Block with SC2 since day one and haven't had any trouble running it. But I can tell you that when the game runs the number of blocked connections jumps.