Don't take what I'm about to write as disagreeing with you. It is more about the thought process that went into my choice to use CGI::Ajax for the example. Your points are strong, although possibly not complete: You've validly pointed out that clarity and 'non-intrusiveness' suffers in my example. What you missed is that it traded it for performance.
Not really. You see, performance and size tend to be my primary goals because I frequently need these kinds of scripts to be used on web pages that both receive many hits per day and that are already overly heavy byte-wise.
So my goals of "runs fast, loads fast" compromised with the goals of "code clarity, full featured" to settle on CGI::Ajax for the example to get "Ajax clarity, acceptable performance".
Code clarity would have argued for using one of the major JS toolkits. Performance would have argued for eliminating CGI::Ajax entirely and not using a toolkit library.
Similiar issues arise using the off-the-shelf Ajax libraries. They add dozens to hundreds of Kbytes of stuff needing to be loaded by the web browser (with dramatic performance consequences resulting just from that fact). Additionally, they tend to run slowly above and beyond that (Digg is a classic example - they use an off-the-shelf JS Ajax library that causes my machine to bog completely down on their longer pages. It is quite annoying.)
So, in addition to your (excellent) suggestion of covering the use of off-the-shelf Ajax JS libraries, I need to cover when-and-why NOT to use them.