The Foundation are hardly good guys. They do do some things which are beneficial to humanity, but they also do an awful lot of terrible things to people if only because the Foundation has practically limitless money and resources, is supported by every civilized country in the world, and the various 05's probably have more power at their disposal than most world leaders. That in mind, there's no reason why they CAN'T do terrible things to people on a near-constant basis.
Unfortunately, the foundation still has a one-up on the GOC, if only in one respect. While the GOC wants to protect the world by destroying the things that can bring about an end-of-the-world scenario, the foundation is actively trying to 'learn' from the things that can bring about the end of the world. Looking at the world that the foundation lives in, SCP's are all over the place. Extra-dimensional entities pop into existence just to fuck with people, items of questionably inscrutable power are found just lying around in ordinary people's homes, mad scientists seems to churn out unfathomable artifacts every now and then 'just because', and there doesn't seem to be any end in sight to the creation of SCP's. With this knowledge, the SCP Foundation is probably the most altruistic entity on the planet, as they're trying to learn WHY all these things are the way they are, and if we do, then a whole new spectrum of possibilities opens up to mankind. So go ahead and sit back and call the Foundation a bunch of evil bastards, but when an Eldritch Horror from beyond the stars opens up a portal on the moon, and he sticks his head out and sings the song that ends the Earth, the SCP Foundation might just interrupt him, going "Oh hey, look what we found out!" and then they use some extra-dimensional technology (learnt from the various SCP's) they rigged up to throw all his evil magic back in his face.
I don't think the GOC is willing to do what it takes to preserve humanity from the unknown, is what I'm trying to say.