I agree with you that the speaker should be told. Contrary to other aspects of a talk (slides clarity, order, etc..) which are somewhat optional and left to the speaker's interest in making a good talk, intelligibility of the speech is a minimum requirement. Not taking care of this is probably hurting him badly. 

Last time I attended in a very similar situation one of the more senior speakers approached the unintelligible speaker and flat out told them : "Do you know it's very hard to understand you when you speak"?. I was there and made a little joke to lighten up the comment and we walked away but the speaker most likely got the message. 

So, there's one way. If you do not have the seniority required to give unrequested advices in person tho, your suggestion seems fine to me. Send an anonymous email explaining that you had a very hard time understanding the talk. Just make sure you are passing out the right message, that you are trying to make him aware of what you felt was a big issue making communication difficult and not shaming him for it. 

As to what  people have said in other answers :

1) the speaker might be aware of the issue, but not of his severity. This might give him the push he needs to act on it. 
2) there's plenty of free and little time consuming ways of improving pronunciation (movies, pre practicing talks, YouTube videos) 
3) I don't think you are 'shaming' him, no one asks for British English in academia and accents are usually never questioned..as long as they can reasonably be understood