If you must start with "My favourite fruit", then the form that I would recommend is "My favourite fruit are apples."
By the same token, "My favourite food are oranges."
A single subject can take a plural object via a PLURAL noun. For example, My favourite race are the Chinese people. My favourite music are the Bach concertos.
I think many grammarians have discussed this, and this seems to be the primary position of Fowler and his ilk. Fowler remains today a major authority on English usage. The book "Fowler's Modern English Usage" is regularly updated by experts at the Oxford University Press. H.W.Fowler died in 1933.