So, now that the zip file is missing from GitHub, some people are starting to upload it elsewhere. Can the people who got it from GitHub earlier post the result of running md5 Atom.zip ? That might help mollify the paranoid conscience. (EDIT: or any other hash function for that matter.)
I think the atom.zip is being updated continuously. Today I finally got my invitation and it gives a different shasum too. File diff shows the Info.plist of my newly downloaded version as of 2014-03-07 is:
CFBundleShortVersionString
0.69.0