Yes, via Old French benigne.
The meaning changed in modern French. Une tumeur bénigne: a non cancerous tumor. Bénin/benigne is not "kind" anymore, but means the opposite of serious, severe. (it's another way to be "kind" finally)
English has both meaning of benign. Benign as kind, but rare as very very formal. https://www.oxfordlearnersdictionaries.com/definition/american_english/benign
And benign as "kind" in the cancerous way...
(Classical) IPA(key): /beˈniɡ.nus/, [bɛˈn̪ɪŋ.n̪ʊs]
(Ecclesiastical) IPA(key): /beˈniɲ.ɲus/
Classical could have a hard "iɡ.n" pronounciation.
The pronunciation of this hard "ɡ" is here:
(I don't see differences between [g] and [ɡ] personally.