I recently read a criticism of the use of protagonist in the plural because it is derived from the Greek for first actor. It is commonly used in contemporary English in the plural for the main people involved in something, whether actors or not. The person making the criticism asked if there could ever be more than one first actor, which makes me wonder who would be the first actor in a Laurel and Hardy film.
I don't feel that a word has to follow its origins slavishly. If we wish to use it in a slightly different sense from the meaning in its original sense, then why shouldn't we? Once a word becomes a loan word, it takes on a new identity and a new life in a different language and is perfectly capable of acquiring new meanings or shades of meanings. 'Anorak' is derived from an Inuit language for a typeof coat, yet has come to mean an obsessive, through association with the image of computer geeks, which strikes me as an interesting development rather than a problem.
Language Poll: http://www.usingenglish.com/poll/352.html
Last night, after posting this,I went to bed and started reading Simon Winchester's The Surgeon at Crowthorne, a book about the making of the OED (Oxford English Dictionary) and, coincidentally, found that the OED gives protagonist in the plural in its earliest quotation, from John Dryden in 1671, suggesting that it has always been used in this way in English, though Fowler suggests that the plural would be absurd.