The previous (lets call it "version 1") wrapper (before GOTD adopted "version 2" Themida) also encrypted and packed the setup program inside the GOTD setup.exe.
Scanning the downloaded V1 setup program also was unable to look inside the developers setup program. Scanning any GOTD download would just indicate that the GOTD wrapper didn't look like malware. But no users were able to scan the wrapped software beforehand either.
So effectively there is no difference in actual safety in that users cannot scan the downloaded file - as previously scanning the download was also an essentially meaningless exercise. (Of course some users got a toasty warm feeling, that they were doing something useful in scanning the GOTD download - but it served little purpose).
The unwrapped developers setup program is thoroughly scanned by GOTD prior to wrapping (a lot of their reputation rides on checking these files prior to release). For users who do not trust GOTD to scan the files they receive from the developers, it is their decision to download or not - but to date there have been no confirmed malware issues that I am aware of (plenty of false positives, and contentious definitions from users of what constitutes "malware" - like changing a home page, or an option to install a toolbar)
I would suggest that if you wish to install a giveaway, and you are able to, disable your antivirus during the installation, and enable it again once the software is installed. Many Antivirus apps have a real time option where the system is monitored and files are scanned as they are accessed and programs are run.
Alternatively install a secondary (normally disabled antivirus) that you can enable while ESET is disabled. Something like Microsoft Security Essentials (that I run) does not complain about the GOTD installer.
As for novice users being unable to disable (or use) their antivirus, this really isn't GOTDs charter. Sure we (the users) could create tutorials for each antivirus product on how to enable/disable/scan/update etc etc - but surely this is something that should be fully covered on the AV product site & documentation. There are multiple posts/comments each day of users announcing that the GOTD has a virus or malware "because their antivirus product said so", when thousands of others (including the GOTD team prior to release) have managed to install the software cleanly. There is no getting away from the fact that using security software, and installing/uninstalling applications (including what to do with a zip file), is something that may require some reading and research. Perhaps Themida and the need to change/disable the antivirus software during an install, will introduce and require some new skills... but the day you stop learning you are dead.
On a separate note:
Regarding the "who digs the elephant trap" article that has been posted numerous times by users on GOTD, it is also worthwhile to read the comments that follow the article. I believe the article is purely from the Antivirus (McAfee) viewpoint. Historically they identify viruses by looking inside files (yes this is oversimplified) and looking for a familiar signature. Themida prevents this - and as such has, in the past, been adopted by virus and malware writers. The solution by some AV companies is to just flag EVERYTHING with Themida as being "suspicious" or "possibly unwanted". They don't actually come out and say it is a virus (because they cannot). Rather than adopting other ways to detect malware, they simply state that people should stop using Themida - which is an easy thing to say, when it isn't your own product that is affected by such an action.
Other products that operate differently operate based on what a program does - effectively they look for suspicious activities being performed by software that the user hasn't previously explicitly marked as trusted. Some applications that do this (or similar) include:
http://spyshelter.com/
http://softsphere.com/
http://www.arovaxshield.com/ (FREE)