Good answers. You seem to have alot of though put inot this already. That's a good thing!
If you really want to run with the technology scheme maybe you could use Heed the Wisdom of the Ancients and run the Techmarines also. You could explain it in that the Adeptus Mechanicus have turned their back on them and the chapter has taken the knowledge into it's own hands.
If the believing that the Emperor is not a god, but only a great man is what has them on the brink, it's not that well thought out. Many chapters have this belief, the Salamaders Chapter chief among them who do exactly what your talking about, but still get Adeptus Mechanicus help. You could use the Adeptus Mechanicus representaive on the High Lords Council as the bad guy pushing for their excommunication. The rest of the High Lords don't see a legitamate reson for it, as they know the Adeptus Mechanicus themselves keep many secrets, and don't follow through with a large enough voting to ensure the chapter's destruction. This would fit in rather well and give you points to use later in campaigns and fluff writing.
Anyway, your on a great track. Some secrets for a chapter are fine and dandy, just try not to get lost in them. I hope to see more of your fluff in the near future, as I think your setting on a truely remarkalbe take.
You might want to look at my
DIY Chapter as well, maybe there is something I missed that you could expand on!