Found it! (My edition is the 1969 small Penguin, 1982 reprint). Where does Prebble quote this, and who does he quote?
There are two index entries for Religion > Catholic; 137 has the "contributory cause" section quoted above, and 175 is a discussion of the last wave of emigration from Knoydart, where "They were Catholics, for the most part". However, it and the subsequent pages don't seem to draw an obvious link between that and the motive for eviction, which is presented as economic. 
I simply can't agree with your thesis, which is that there was systematic anti-Catholicism not recorded at the time (despite anti-Catholicism being common and widely seen as acceptable in the nineteenth century) and not discussed by historians now, but secretly hinted at instead, for reasons that are clear to you and not to me.