Executing prisoners would have garnered him more public anger and hate. He got away with executing Salaad Gabeyre because it was early days and Salaad had many enemies.
He once imprisoned the Manifesto signees in early 1990 and sentenced them to Death, the whole of Xamar almost came to a halt that shook the regime so much they had to reduce it to imprisonment. Don't under estimate the public support.
Honestly, Caydiid had it too easy till the UN came. Afwayne use to give stars to reer baadiyo geeljirayaal who have never picked up a gun and told them to protect his govt

ma waxaasaa layska dhici karin
If he was a smart leader, he would have built a loyal Army across clan lines. Instead he got paranoid when the Mj's attempted a coup and he saw many regimes in Africa overthrown by Vice Generals and Army Heads. From that moment, he surrounded himself with clansmen thugs like Morgan, Gaani, Gabyow, Dafle etc. He was even willing to tribalise the economy and gave Xoosh Kibray the only license to export and import without being taxed. How do you alienate the majority stakeholders in the country and expect to rule forever with a bunch of nobodies?