I don't know for sure who the Pope meant, since he did not give very many clues, but I think he was referring to Antonio Rosmini-Serbati (1797-1855). His writings criticising the church were placed on the Index during his lifetime, but he was beatified by Pope Benedict XVI in 2007. The biography fits the way that Pope Francis describes events, with the possible exception of "not so long ago", depending on how wry he was being (and of course, from the point of view of Church history, it's comparatively recent).
A decree of Pius IX on 30 May 1849, reproduced here as a supplement to an 1841 edition of the Index, lists:
Delle cinque piaghe della Santa Chiesa trattato dedicato al Clero Cattolico etiam con Appendice di due lettere sulla elezione de'Vescovi e Clero e Popolo.
La Costituzione secondo la Giustizia sociale, con una appendice sulla unità d'Italia.
-- Di Antonio Rosmini Serbati. Decret. 30 Maii 1849. Auctor laudabiliter se subjecit.
That Latin remark at the end commends Rosmini for submitting to the listing of his books. The same books are listed in the 1900 recension; I haven't tried to trace the history any more closely than that.
These works carry the English titles Of the five wounds of the Holy Church and The Constitution of Social Justice respectively. Wikipedia summarizes the first as follows:
Of the Five Wounds of the Holy Church presupposes an analogy between the Holy Wounds suffered by the Lord's natural Body pierced on the cross, and His mystical body, the Church, pierced by the sins and errors of men in the ages of Christian history.
The five main evils of his contemporary Italian Church correspond, in Rosmini's view, to the five wounds of the hands, feet, and side of the Divine Redeemer. Beginning with the wound in Jesus' left hand, he likens it to the lack of sympathy between the clergy and people in the act of public worship, which he sees as a result of a lack of adequate Christian evangelical teaching. This is to be accounted for by the wound in the right hand — the insufficient education of the clergy, their secularisation and their alienation from scripture and their bishops. This again was both caused and perpetuated by the great wound in the side, which pierced the Heart of the Divine Sufferer, and which Rosmini sees as a parallel for the divisions among the Bishops, separating them from one another, and also from their clergy and people, forgetting their true union in the Body of Christ. The wound of the right foot is compared to the civil power of the Bishops making them into worldly schemers and politicians, more or less intent on selfish interests. The wound of the left foot is compared to events of the feudal period, when the freehold tenures of the Church were treated as fiefs by an overlord, or suzerain, who saw in the chief pastors of the flock of Christ only a particular variety of vassals or dependants.
As indicated above, Rosmini's contested reputation was eventually rehabilitated. Some recent documents of interest:
Aside from the clear continuing interest on the part of Benedict XVI, it's interesting to speculate whether Pope Francis might have found something appealing to him in Rosmini's writings, on social justice and the reform of the church.