It seems like ages ago since I played EFS. I thought it was a great game, but its flaws kept me from playing against my desires...
Like most games in general, the AI is little more than a tutorial opponent. That being understood, I and a freind tried to find 3 other freinds willing and able to play EFS with us. We never succeeded. We did not know of any Internet support, with a pool of players looking to start games.
We made our own mod, starting with the Nova mod, which we called Super Nova. It's a shame we never got to play with it.
IIRC, spies and assasins can attack on Bizantium Secundus before a Regent declares themsleves Emperor.
I'm pretty sure, all you can do to gain black-listed techs is to study them, and be strong enough to defend against the Church's Inquisitors that will inevitably come after your labs.