It was still blatant vote manipulation, but the end result was science AmAs were regularly featured on r/all and also the default view of Reddit.
Yes, morally and ethically, the ends don't justify the means.
HOWEVER, the mods were manipulating votes to bring high profile visitors to Reddit, users were happy, Reddit execs (should be) happy that they were getting big time scientists posting, it seems like the only disconnect is how they did it.
This finger wagging is just PR from Steve Huffman. If they really cared, they would have worked with moderators to create the toolsets to bring in more high quality content, and moderators wouldn't have to resort to desperate measures to bring in more eyeballs.
"We're working on it" is a nothing statement. Instead, they're putting resources into a UI refresh that does not have very much support from the community.
But you have a subreddit who has moderators who consistently organize high quality, low SNR ratio content, and who also depend on the front page to drive a large amount of their traffic. There has to have been a way to seamlessly get the custom tailored /r/popular stuff onto the mainpage without impacting these high content subreddits. I just don't think Reddit really put enough thought into this. Even something sort of hacky like "super mods" who could curate posts onto the front page. In the end, the /r/science mods had cobbled the tools to notice the drop of users (and Reddit staff didn't run enough analytics to gauge the impact of their decision), and the call was made.
I don't think Reddit staff either has the numbers of admins or the tools to adequately make informed decisions about the impact of changes they make.
Subreddits and Reddit are in a symbiotic relationship. Most subreddits depend on the mainpage to deliver them eyeballs. Some subreddits depend on those eyeballs they receive from the mainpage to create good content and PR for Reddit.
Let's be honest, there's wealth of content on Reddit, enough so that users might not miss some content going missing randomly.
<Personal opinion starts here>
However, I personally believe that Reddit should cultivate stronger content than cat memes and animated images. Getting Stephen Hawking to answer questions from the public is, in my opinion (from a site culture and company PR perspective), more valuable than the 1000000th Star Wars prequel meme to appear on the front page.
Though I think a better comparison might be the eating habits one other people have made. Veggies might be better for you, but most people will choose to eat junk food. I just think that's sufficiently solved by natural selection.