From its viewpoint it was a smart political move.

The Saudis are in trouble over their war on Yemen. After nine month of bombing the hell out of the country there is no chance that the aim of their war, reinstalling their proxy government in Sanaa, will be reached anytime soon. Meanwhile Yemeni forces raid (vid) one Saudi town after another. The Saudi regime change projects via Salafi jihadists in Iraq and Syria are also faltering. The low oil price make it necessary for the Saudi government to introduce taxes on its people. New taxes are hardly ever popular.

To divert from these problems the Saudis decided to get rid of a bunch of prisoners and to use the event to regain some legitimacy. Many of the 47 killed were truly al-Qaida types who a decade ago had killed and blown up buildings in Saudi Arabia and wanted to violently overthrow the Saudi government. With the recent anti-Saudi calls of the Islamic State and al-Qaeda a jailbreak or some hostage taking to free the prisoners were a real possibility. Only four of the killed were of Shia believe. One of those was the prominent rabble rousing Shia preacher Nimr Baqr al-Nimr from the majority Shia eastern Saudi province Qatif.

Al-Nimr had called for the youth in Saudi Arabia and Bahrain to raise up against the government. He called for the overthrow of all tyrants not only in Saudi Arabia and Bahrain but also of the Assad government in Syria. He was no Iranian stooge but defended its form of government. Al-Nimr said he was against violence but several of the demonstrations he called for ended with dead policemen and protesters. It was quite astonishing that the Saudi government let him preach for so long. A Sunni cleric in Saudi Arabia would have been put to jail or killed for much less revolutionary talk.

Some dumb people like Human Right Watch's Kenneth Roth say that al-Nimr wanted a democratic state:

Kenneth Roth @KenRoth

Sheikh Nimr's real offense: leading peaceful protests for Saudi democracy, equality for Shia

That is nonsense. A U.S. diplomat talked with al-Nimr in 2008. A cable available through Wikileaks summarizes:

Al-Nimr described his and al-Mudarrasi's attitude towards Islamic governance as being something between "wilayet al-faqih," in which a country is led by a single religious leader, and "shura al-fuqaha," in which a council of religious leaders should lead the state. Al-Nimr, who conducted religious studies for approximately ten years in Tehran and "a few" years in Syria, stated that all governance should be done through consultation, but the amount of official power vested in the hands of a single official should be determined based on the relative quality of the religious leaders and the political situation at the time.

A system led solely by religious judges or clerics is not a democracy. From that interview it also seems that al-Nimr had no clear picture of what he really wanted. His point was to always "side with the people, never with the government" independent of who or what was right or wrong.

The Saudi government's patience ended when in June 2012 al-Nimr disparaged the death of the interior minister and crown prince Nayef bin Abdul-Aziz Al Saud:

He stated that "people must rejoice at [Nayef's] death" and that "he will be eaten by worms and will suffer the torments of Hell in his grave"

That did him in. Al-Nimr was imprisoned and sentenced to death.

There was concern that actually killing al-Nimr would increase Sunni-Shia tensions. Several governments and the United Nations had warned that doing so would increase sectarian strife.

Well, that is the point!

The Saudi government's legitimacy depends on financial largess and on being a sectarian Wahhabi "defender of the faith". Raising the sectarian bar by provoking a Shia reaction only helps the Saudis to rally the Wahhabi Sunni clerics and the people to their side. The killing of a prominent Shia also gives cover for executing the al-Qaeda types. These do have many sympathizers within Saudi Arabia and killing them without killing al-Nimr would have led to protests or worse by Sunni radicals. Even with this cover some al-Qaeda type entities outside of Saudi Arabia are threatening revenge.

The Iranian government and Shia organizations in Iraq fell for the trick and protest against al-Nimr's execution. It allowed some organized gangs in Tehran to storm the Saudi embassy and to set it on fire. In Saudi Arabia's eastern province young Shia protesters violently attacked police forces (vid).

This was exactly what the Saudis rulers wanted and need.

It may also have been what some conservative Iranian circles were looking forward to.

http://www.informationclearinghouse.info/article43851.htm