First:
Then about the religions highlighed in the Boston Globe article:
Yazidis and Druzes are as Abrahamic as Sunnites and Shiites. Also Mandeans revere persons from the old testament and John the Baptist, and are classified as Abrahamic. Yazidism, Mandaeism and Druze religion have not been reliably shown to date back to before Jesus, though they all incorporate older beliefs and practices - just as Christian religion does.

although personally if I were going to investigate how pagan or not-pagan a religious group is I would want to go further than Wikipedia in my examination.
I very much encourage you to do so.

I personally know many duo-theistic pagans today, and even some monotheistic and panentheistic ones, ...
So does the Wikipedia article I provided as a starting point. Perhaps you continue further studies from here?

clearly Thabit ibn Qurra would have died centuries before the setting of Ars Magica as an individual, but the idea that sects, especially small sects, would have existed under Muslim tolerance is not exactly far fetched.
To be eligible to be Dhimmi in the middle ages, you had to be recognized to belong among the People of the Book. This was often a political as well as a theological classification, as can be seen from both the Sabians of Harran and the Hindus under Muslim rule. But it certainly required some interest by the Muslim rulers and scholars to find a position for a sect or religion under Muslim rule, which puts small sects at a significant disadvantage.
The last reference to Sabians of Harran I know of is in the name of the eminent Muslim astronomer Al-Battani - but there may of course have been others.
A elusive and resilient pagan underground cult that might interest you is the worship of Dhul Khalasa. Some claim that it resurfaced from hiding or resurrected somewhat before 1815, only to be destroyed again by gunfire. If it made it somehow into the 19th century, it certainly was never accepted by Muslims. This cult may serve well if you need medieval Arab pagans for your saga.

Though really zoroastriansim was polytheistic seperating a pantheon into "light" and "dark" camps rather than bein duotheistic, so the lines are rather blurry here...
We had addressed Zoroastrianism on the forum before: see here and especially here. Qualifying it simply as 'duotheistic' or even 'polytheistic' is not helpful.
Cheers