Yes, I think he was Nestorian in a sense, but for that matter the whole Assyrian Church was after the council of Ephesus in 431, because they refused to denounce Nestorius as a heretic. Their Christology eventual was worked out by Babai the Great (c600) - stating that Christ had 2 essences, unmingled, but eternally united in one personality. Isaac came after this in the 700's, so he wasn't directly involved with the Nestorian controversy and would be followed the teachins of Babai. Looking back on it now, it seems like most the controvesy with the Assyrian Church was due to language difference. Basically, when the Greek terms were translated into Syrian, they didn't mean quite the same thing to them. It's my understanding that the Assyrian Church is in dialogue with the rest of Eastern Churches and may sometime come back into full communion with them.

As far as quoting him - I always think that nothing can be taken out of context. The writings of the saints and fathers must be taken as a whole, and not piece by piece. Truly, St Isaac said some great things, but I wouldn't base my entire theology on his writings. I see people quote Origen all the time too, and many of his teachings were condemned. So, you just have to take it for what it is and be sure to test what is being said with what you know about Orthodoxy.

If Isaac was indeed a member of the "Nestorian" Assyrian Church of the East, how did he come to be canonized in the Orthodox Church, and how can this be canonically justified?