There's two ways to do that. One is to not allow StoryProgression to automatically place inactive sims into the specialty schools and make that a manual, the player gets to decide in each case process so the rabbitholes you don't want acting as schools do not get any students (this is actually how I play my worlds).
NRaas > SP > General Options > Options: Careers > Options: School > Auto Assign School > False
The other way is to open the Careers School add-on module up in S3PE and deactivate or remove the science center school data. The module is really just an XML tuning file for the Careers mod. Otherwise wherever you have a science center, and you can have more than one per world, you will potentially have a school.
But I would vote for finding science centers that behave themselves better, given the choices. I still claim that, by chance, none of the science centers I use for schools in any of my worlds have this issue. Two of them are even combo rabbithole buildings with hospitals. Combo rabbitholes used to cause all kinds of issues for us, but thankfully those all got fixed with Overwatch years ago. In heavily populated worlds though with lots of sims using the science center/hospital for various things, that does make for a very busy rabbithole building.
