First of all I'll jump on the bandwagon and say that you should make sure to talk to the guy before you initiate this kind of plan. If you've already done that, and he's failed to "get it", go ahead.
With that said, I'd suggest that you make it a point to design your own stuff, and leave the established canon and metaplot etc. as background noise. Basically make the world your own, effectively making his metagaming more or less useless, because he never knows which parts will be real in your universe, and which will not be. And even if something's real, it's by no means certain that it is in any way connected with your game.
As for the the charity group you consider, I'll echo the idea of making them an actual charity. And then tie them in with a bunch of different power players. Some politicians, some very rich filantropists, the Mafia, the Yakuza, and maybe a local branch of Aztechnology. As suggested you might also throw in a couple of Ghouls, who just happen to work there, i.e. as night guards and unskilled labour. Add a shady character to the staff list as well, and have the guy have a little side job pushing drugs to the people that use the charity. Maybe let Aztechnology use the charity as a testbed for some products, not all of which might be entirely safe or thoroughly tested yet. Maybe one of the filantropists are connected with a Humanis group in some way (as in he's friends with a couple of members, and have been to a couple of their events, but don't share their views...). As for the politicians, they can be as shady and corrupt as you want, and maybe one of them are connected with a bug shaman who also works at the charity once in a while doing some quite legitimate work. But despite of who's bankrolling the place, keep it a genuine charity, and let the media and all of the "investors" go nuts, if the player(s) go in and blow the place up.
If you set things up so that the player will have to go in and abduct one of the staff members or something similar, you could have the aforementioned bug shaman at work the same day, and start throwing ugly stuff at them, as he tries to protect his colleague. Also, you might have some of the homeless have a go at them, as the targeted staff member is a well liked individual, and some of the people there get pissed when he or she is assaulted by some violent thugs...
Basically, give them a good chance to misinterpret stuff at every turn, unless they dig deep enough to realise that the shady looking things that turn up initially, is related to the backer, and not the charity itself.
Have fun, but make sure to give the players a chance to play catch on, if they are smart enough about it, and don't just jump to conclusions