Network policy on comments has always been that there has to at least be some bare minimum contributatory (contributionary? contributing?) nature to it. That's why they have a reputation requirementThat's why they have a reputation requirement:
So by the time they earn 50 rep, they should have learned roughly how things work, and be in a position to offer a useful comment and not a "+1 AWESOME ANSWER" sort of comment. - Jeff Atwood
An earlier discussion on Meta Stack OverflowAn earlier discussion on Meta Stack Overflow, less about deletions but more about good comments, sheds some light into this particular scenario. I won't point at any particular answer in that thread, but rather, the general sentiment expressed in nigh every answer.
Support is good. I think everyone appreciates being told that their question or answer is helpful, that someone is finding their content meaningful in some fashion. But we have a resource to perform exactly that - upvotes, which are possible long before you gain the privilege to post comments on the vast majority of the site (and on anyone else's questions, for that matter). They indicate to the author of the post, that a user has found their stuff useful (and in the context of the site, they give a little more bonus to the user in the form of reputation).
Usually, these kind of comments get flags on other sites, if it states nothing more than a rough equivalent to "I love this answer!". Had it a smidgen of maybe a "why" or something else to add, even if just to get a wry giggle, then I don't think it would've been struck so fast.
I hope it's understood that in general network policies, this kind of deletion is not about censoring courtesy or silencing compliments as much as it is just removing something that can be considered redundant and non-contributing.