The question is not that if he was a bastard, but if he was an intelligent bastard.
The deaths of the Civil War (and the post-war trials, and the apalling conditions in that the republican prisoners where kept (even Himmler thought that they were too harsh)) could be justified with propaganda (even now there are people who swallow the Francoist version of the Civil War hook, line and sinker), and using the carrot and stick strategy with the pressumibly hostile sectors of the populations (see the treatment of the Basque country pre-ETA).
Deporting the population of one of the most developed parts of the country, where a important part of the population had supported the military coup, it wasn't as justifiable over the eyes of the falangist-conservative-carlist conjunction of interests that supported the regime (Carlists and conservatives were strong in Catalonia, by the way)