The Spanish investigation is not premised on universal jurisdiction in its purest form, at least not yet. The proceeding arises primarily because America held five Spanish citizens and residents at Guantanamo, including one who later escaped criminal conviction when Spanish courts found the evidence procured against him at Guantanamo "totally void." So if the allegations are true, Spain actually has its own dog in this fight: harm done to its citizens by foreign criminals. That leaves this prosecution on substantially the same footing as a U.S. prosecution of the mastermind of the Cole bombing in Yemen (because the victims were American) or the recent federal conviction of Chuckie Taylor for perpetrating torture in his father's country of Liberia (because the defendant is American).Not that I think universal jurisdiction is any more incorrect in the case of torture than it is re: genocide.
At the Daily Beast, John Sifton observes that top CIA officials have a lot to lose by further investigation of their torture program, and speculates that Leon Panetta is supporting a cover-up at their behest.