I don't quite understand, in what way were you penalized? Swallow made it clear how the system works: you sign up, you get put on the waiting list. What happened in your case is highly unfortunate (and as I said previously, I feel bad for you), but Swallow can't make any exceptions. He can't go ahead and tell the teams that've already signed up "Ok, we're moving you down because these guys didn't have the opportunity to sign up." Regardless of what you're going through, that simply wouldn't be fair to those teams.
Just sign up as soon as you can, and it won't be that long a wait. Hell, my team signed up immediately, but the seeds are so messed up that we'll have to wait for like a month after week 0. Teams that sign up now could potentially get a shot at the challenger's Cog before us.