This is the order I did it in:
first I changed the descr_sm_faction.txt entry and tested it.
then removed the superfaction line in descr_strat.txt and tested it again.
I was still getting the messages from the senate, so I changed the core_attitudes stuff at the bottom of descr_strat, but I still got the messages.

I have no idea why they still keep popping up though. I went about 10-15 years in but the messages keep coming. The thing that is even weirder is that my characters got elected to quaestor, praetor and censor, even though they didn't do anything the whole time and I was losing popularity with the senate.
Is it possible that the senate faction is hardcoded to give factions with the roman_ prefix missions?