This area is getting increasingly blurry.

(1) Traditionally, the subject pronoun followed the copula: 'it is I'. Nowadays, 'it's me' is gaining in acceptability.

(2) However, also traditionally, the case follows the case of the (pro-)noun complement: 'he had loved whom?-- he had loved her'. Nowadays also, 'who' is gradually replacing 'whom': 'Who do you love, tell me, who do you love?'-- yet this does not mean that the referent pronoun is similarly effected.

(3) That leaves us split like Solomon between 'she' as the formally correct complement of 'be' and 'her' as the formally correct referent for 'whom he had loved'.

(4) Pronoun case, as Greenbaum & Quirk observe, may be 'concerned more with subject territory (the pre-verbal part of a clause) in contrast to object territory (the post-verbal part of a clause)' rather than strict grammatical distinction.

(5) Where does that leave us? Well I know which one I like, though I may be damned for it: 'It was she whom he had loved', -- 'she' is at one and the same time the complement of the copular verb 'be' and in pre-verbal position vis-à-vis the relative clause. Two good reasons to think the 'she' form is more 'correct'. Now, if I could just do something about that 'whom'. . . .