An interest in puns has led me to start reading the literature on homophones. Interestingly, in appears that in the scientific literature "homophone" and "homograph" mean the same thing, which explains why there are so many papers about mispronouncing homophones. Here's a representative quote:
"...reports a failure to use context in reading, by people with autism, such that homophones are mispronounced (eg: 'there was a tear in her eye' might be misread so as to sound like 'there was a tear in her dress").'
Sticklers will note that "tear in her eye" actually does involve a homophone (tier), but I don't think that's what the authors meant.
Readers of this blog know that I'm not a prescriptivist -- that is, I believe words mean whatever most speakers of a language think the words mean. So I'm not going to claim that these authors are misusing the word, since there seem to be so many of them. That said, it would be convenient to have a term for two words that have the same pronunciation which is distinct from the term for two words with distinct pronunciations but are written in the same way.