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I think you should have to hire dedicated researchers to be able to research. (Special thanks to common sense for the idea hehehe)  They die during testing, The higher threat level (Safe, euclid, keter) the more chance of death.  Also if a breach occurs, You should have to pay ALOT to recontain it. (Exact costs based on threat level) Because, if this facility was real, ALOT of money, resources and effort would need to go into recontainment. (NTF Deployment, Potental casualty's of agents, Amnestic deployment for civilians, cover up for civilian deaths, etc...) So if a breach occurs, you suffer the consequences.  

Apologies for a late response, but I've only just noticed this. I will definitely take these ideas under advisement. Unfortunately I've done a somewhat silly thing and overwhelmed myself on what exactly I'm doing for the next update, but when I do get the time and attention to figure it all out, it shall be awesome. xD

Also i have another idea: Thaumiel SCPS. according to the wiki, Thaumiel SCPS are SCPS used to contain OTHER SCPs.  IDK how this would be implemented.