Is there anything to do to prevent the Horatios from assimilating everything they find? In my current game I had set minor factions to hard and had plenty of them, but the AI Horatios took most of the over in a very short time. I'm currently playing on Hard difficulty btw.

I think the quests should be made harder to perform; most of the quest are rather easy to do once we pay for the assimilation...

Well, the horatio collection bonus sends 5% of food production to influence. Horatio tend to produce quite a lot of food, which leaves them with lots of influence mid to late game. This results in a quicker buyout for minor factions. I for one have more of an issue with Lumeris buying minor factions with dust really early on, since that happens more often than horatio sniping my minor factions. 

I haven't looked to see what happened, but I was playing a mp game with a custom Horatio, about half-way through the game all of my interactions with the minor civs were free... Probably a bug, but let me tell you that was nice, sure praise them 10-15 times for free, turn, assimilate for free. 

Really helped grab some extra bits and pieces of peoples =)