To make it clear: in the Esperanto movement "krokodilo" means a person who speaks a native language among other esperantists or a language that not everybody can understand. There is also a verb for this - "krokodili".
"Aligatoro" means a person who speaks foreign language among esperantists in order to practice that foreign language, because quite often Esperanto meetings are international. There is also verb "aligatori" for this, and noun "aligatorejo" that means an event, organized by esperantists in order to practice foreign languages.
Of course "krokodilo" and "aligatoro" can refer to the animals as well.
I think when people use the term "corruption" in a linguistic sense, it's not to denote that the change is bad, just that a change came about somewhere along the line, usually due to human error or mistakes.
I don't know for certain whether or not the word "alligator" came about as a mistake, though, or whether it is just a result of natural evolution.
Aligators have the eyes closer and taller while crocs have a more flatter head. I believe crocs have a stronger bite, so I fear them more, but wouldn't survive any of them anyway. In Brazil we do have different words and I think one of them is native here, but as a cityboy who never saw any out of the zoo, I would take my words with more than a grain of salt.