Regretsy uses "derp" as an insult. Granted I don't know the age of the person who runs that blog, but the audience is large enough that I think it can be used as an example of a current usage where the intent is not to be affectionate.

I'm not in the MLP fandom so can't comment on the origins of the term there. But given that it's easy for those of us who know the negative background of the word to see why the pony in question would be - pardon the expression - saddled with the nickname I think it's not so much that the word changed meaning as that some people using it don't realize how insulting the word is.

Put another way, while some people are using "derpy" to mean "adorkable" I don't think adorkable things would automatically be defined as derpy. Nobody's calling a cute baby pony derpy, they're calling a pony with cross-eyes derpy. Even affectionately it's being used to highlight what makes the character seem odd.

Plus, IMO, even with all the affection in the world an insulting word is an insulting word. Kind of like using the word "midget" instead of "little person." Someone might not be familiar enough with the history to understand why "midget" is considered derogatory and therefore might use it with the best of intentions, but once the history is pointed out to them they should change their terminology (or come to terms with the fact that people are going to think less of them for not doing so).