I wrote the SCP foundation in a fairly negative light in one of my WIPs. If this foundation we're to exist in the real world, and the public knew about it, I can't imagine it'd survive long. You have the issue of subversive characters with access to some of the most deadly and powerful creatures, killing and abusing convicts (death row or not), imprisonment and use of various entities that may not always be of risk to the public, and an elite group of higher ups that work in the dark.
I'm new to the site and maybe I don't understand the cannon well enough, but to some extent the foundation sounds like a Mary Sue or a white knight. Then again, it'd be understandable that the site wouldn't publish their critics on their scp site (the scp wiki since its supposed to be a database). Nonetheless,the alter foundations that do challenge the SCPF are almost always written to be extremists or rampant occult religious organizations that want to rob the SCPF of their SCPs for personal gain (an easy antagonist and foil). I think the foundation is more interesting when you look at it as a morally gray group that believes they have all the answers, an organization that claims to value and protect humanity while disregarding their lower class personnel's own safety, a small group of elites willing to throw away the lives of their workers for the sake of knowledge and power (union time baby!), anyways I just think reveiwing the wax and wane of the foundations ethics is an interesting discussion and i've only really seen folks defend the SCPF's actions when discussing their morality. wait am i posting this to the right place