This is a really interesting bit of speculation. Obama's consistently "just off" statements (i.e. saying an executive order that hadn't been implemented yet would have protected Snowden) make me think that Obama & his advisers doesn't have a good handle on what the NSA is doing and how the law applies to the "secret state." One could say that "Obama is lying," which may be perfectly true, but it could also be that the politicians are genuinely uninformed and/or think protections exist that don't.
I could see this being the case because politicians train to talk about health care and the economy, while the details of NSA programs are rarely discussed and so politicians have little incentive to be up on the facts.
There's no way Obama didn't know. Remember that Obama just appointed James Clapper, who was caught lying to Congress about there being dragnet surveillance on the American people, to a committee to investigate the NSA and make sure these programs are in check. If he didn't know, it seems like he would be rather pissed at Clapper and reluctant to let him investigate his own agency.
I don't think it even has to be that extreme. When one starts out as a politician, even small-potatoes stuff like inflated tax exemptions would be enough to influence the ambitious. Later, once one is president, they have recordings of all the noxious shit you've done at their command. This is basic spy agency tactics.
It's quite probable that Obama knows about shit the various agencies have done that would make GG's hair curl. It's also quite probable they've done much worse shit that he doesn't know about.
I could see this being the case because politicians train to talk about health care and the economy, while the details of NSA programs are rarely discussed and so politicians have little incentive to be up on the facts.