In my own TL (see signature), I think the ground is set for a surviving and thriving Samaritan religion. The fundamental divergence is a combined series of ethnic revolts (in Egypt, Judaea, Samaria, Galilee) and social revolutions led by a radical Christian group against poverty, declining living standards, inequality and the establishment of the unfree colonate, all happening together and co-operating during a period of most intense external pressure during the Crisis of the Third Century.
As a result, my TL ends up with a division of the Roman Empire; the South-Eastern third becomes a democratic federation of various differently structured local polities. One of them is the Kingdom of Samaria, a moderately theocratic state of the Samaritans, socially less progressive than its immediate neighbours, but relatively stable and loyal to the confederacy.
What follows is a Late Antiquity with more peace, long-distance trade and prosperity, some technological innovations, more political upheavals and transformations, new religious groups emerging, but neither gaining hegemony over the others. Samaritan religion and society, being ethnically entrenched and non-confrontative at the same time, should have no problems as long as this broader setting remains in place.
What can be transferred to other, less revolutionary (or far-fetched), TL ideas? I think two things:
- All the smaller religious groups of the Middle East (Samaritans being just one of them, just think of Mandaeism or Yazidism) have bad chances in large, religiously uniform empires, but also in equally large, religiously pluralistic but socially oppressive empires.
- At the same time, they are just too small to rely on independent polities of their own.
- What you need, then, is a strong, overarching polity which is truly tolerant of religious and social plurality under its roof. Other than my Confederacy of Free Citizenries, examples from OTL which go in this direction are the Achaemenid Empire, the Khazar Khaganate and a few others.
If you can install such a polity or series of polities in the Middle East, instead of highly intolerant Orthodox Christian Byzantium, Muslim Caliphates, Crusaders etc., then you´ll have a much more colourful Middle East, including a surviving Samaritan religion. Samaritan (and Druse, and Yazidic...) rules against inter-marriage and proselytisation are what is demographically killing them even today, but these rules were just survival mechanisms in intolerant empires....