Re: My response
The problem isn't that it "writes log entries as root by default" (anyone can write system log entries without being root); the problem is that it (a) runs as root, and (b) someone has been sloppy about munmap'ping null pointers. This shouldn't really be a problem, but the concern is that another program, which is not running as root, might somehow be able to take advantage of this, and get atop to run something on its behalf, in which case non-root program #2 owns the box.
The moral is that if you've got something you don't know about running in the background, and that program is running as root, and you have concerns about the code quality, then you should stop running that program. Seems fair, and RTFM doesn't really help in this case.
Oh, wait. It's just occurred to me that every time I run Task Manager I see hundreds of these things. Damn.