Could a significant religion have seceded from one of the great churches since Christianity emerged ?
Well, I think Rastafari is the best exemple on how a religion based on Christianism, but not definying itself as such and being obviously distinct could emerge, at least in contemporary times : a reaction against colonialism and/or imperialism, translating itself into a core belief.Vaudou or Santeria could be considered as such as well, altough probably more sycretic religions, than issued from Christianism.
I don't really see why you couldn't have different allohistorical exemple of such reaction.
For medieval and modern times, it's a bit harder : Christianity is a core part of identity, and while you could split off the institutional or official church, you still tended to consider your new belief or church as Christian, if not more Christian.
I could see,tough, Spiritism as understood in the XIXth, becoming a sub-branch of Abrahamic religion with enough syncretism and codification. It was relatively influential and popular even among some lower classes at some point. You can arguably point that in some countries, as Brazil, Spiritism did worked IOTL as what we'd call now a "new religiosity", but I think it could be more strong in Europe with enough changes.