The competing factions, which stretch across the military and politics, pursue a tit-for-tat vendetta that was further reinforced by the recent election — the third vote since 2012.
"Only the rule of law and the depoliticisation of the security forces, as well as harnessing of regional support, could end Lesotho's troubles," political analyst Nthakeng Pheello Selinyane told AFP.
Selinyane said a key player behind the unrest was former army chief Tlali Kamoli, who was sacked in 2014, then led soldiers in an apparent coup attempt where they seized control of police headquarters.
Kamoli was later reinstated before being forced to retire last year.
"Kamoli was openly voicing hatred towards Prime Minister Thabane ... while enjoying the opposition's cheers," Selinyane said.
A SADC report into the 2014 crisis stated that the Lesotho military had a "disregard of civilian rule" dating back to a coup in 1986.
The new government admits the army has held the levers of power in Lesotho, a country with a population of just two million.
"The military can only be brought to order through the unadulterated implementation of the SADC recommendations on reforms," Home Affairs assistant minister Machesetsa Mofomobe told AFP.
SADC has since sent a rapid-response team to Maseru to investigate the shoot-out, expressing dismay that the region's high hopes for the election may have been dashed.
"From the SADC point of view, we thought that the Lesotho problem had ended" with the election, said South African President Jacob Zuma, reacting to the army commander's death.
Stable government would help Lesotho tackle its gruelling poverty and the world's second-highest HIV rate, but its politicians and military look set to be preoccupied by in-fighting for years to come.