I think it's better not to remove the re-direct since the old site was one of the best in its category, reaching around 40.000 visitors/day. As far as i noticed, the "change of address" in WMT wasn't active anymore on the day of the first penguin, when the brand domain was hit. Also, in WMT, the backlinks to the old site weren't showed for the brand domain profile. Now, after verifying the old domain again in WMT, the backlinks for the old domain are appearing again in the brand domain proile. In all this time the 301 was active from the old site to the brand site. What I can easily notice is that Google MIGHT ONLY associate the backlinks from the old site to the brand site when they are both verified in WMT and the "change of address" option is used. Its the only way I can explain the backlinks for the old domain not showing anymore in the brand domain profile after the old one wasn't verified anymore although the 301 was active.