You have to take into account that this is not a military uprising of a few people, its a pacific protest from politicians who represent almost half of the Catalan votes.

There are plenty of examples where people have been pardoned in Spain for more ethically questionable reasons [1]. This, in contrast, is a clear case where it should be resolved politically, not through the legal system.

[1] https://civio.es/el-indultometro/2013/05/06/saenz/