Allowing a whistle post-judgement would be a devastatingly bad idea. Incorrect whistling has always been a problem (there was a period where a group targeted me and mass-whistled all my flash, none of which broke any rules), and letting anyone whistle a flash at any time would result in any controversial flash, or a flash made by controversial authors (say, IWP or the KK) getting flagged.
There are a few better solutions that I could think of.
1) Portal Mods. A handful of active portal users who are also trusted whistle users (some of the top people on the top 300 B/P list would be excellent for this; I know that I'd be happy to help in any way I could) could have the ability to whistle things after judgement, or pull them completely by themselves. They could also possibly re-name flashes and remove the flash's icon.
To limit abuse, maybe these abilities could only be used for the first week in a flash's existence.
2) Inability to change the flash's .swf/title during its first week of life (and longer if it wins TOTW or underdog). I'd be a little hesitant about the .swf thing...some people legitimately upload the wrong file, and have to change it, but it might be a sacrifice we'd have to be willing to make.
3) Vote limitations. Any flash artist who's in the know about the portal knows about the TOTW fights. Massvoting like crazy. This could be limited if, during a flash's first week of existence (or at least until that week's awards are picked), if people could only vote ONCE on it. It wouldn't stop those with proxies that could bypass detection, but it would nonetheless help.
I'm all for innocent fun and games, and for the rights of the artists to do what they want, but there MUST be something new to stop the flagrant abuse that gets past detection.
I'm sure there are more solutions, but these are what I've come up with after spending a long, long time in the Portal (and as a former member of a certain former 'troublemaking' group, I have a fairly good idea how they work, too). Hopefully something will be done, because yes, it is out of control. I've taken a break from B/P'ing lately, but with things as bad as they are, I may come out of my semi-retirement.