No, they sided with the republican powers-that-be because they took active part in the republican government at the time, same as anarchists and hardcore communists. The republicans were extremely inclusive when putting together a government, and left no sector of society unrepresented. By this I do not mean they agreed with their ideals, they just felt that by bringing together all these ideals they would be able to fend off any military unrest. Needless to say it did not work.
I mean, the fact that Franco's idea of Spain was very monocultural (and very much in favor of restoring power to the Three Pillars of Society, namely: the church, the military and the upper classes) did not help, but the fact remains that many in the PNV and ANV (both nationalist parties) were ardent supporters of fascist ideals, and even the "father" of Basque nationalism, Sabino Arana Goiri, was one of the worst racist idiots I've ever read in my life, spewing vile against Jews, communists, et cetera. Back then the so-called leftist nationalist movement did not exists or had very little popular support.