What it is morally is debatable. Many in Section 31 believe they are they are doing everything they can for the Federation, a Federation that is a child compared to them and needs to be managed from the shadows for its own good. Others are probably getting off on the secrecy and self importance. And like in any organization some are probably there for personal gain, not money in this century but information and influence.
Marcus appears to be motivated by an ideology of war, go on the offensive now because of the inevitability of being attacked. Vulcan was pacifist and look where it got them.
granted the federation is still relatively new (they were what? a hundred years old by the end of Into Darkness?) but still section 31 should have been disbanded. it cause nothing but trouble.
Hopefully, this incident brings them out of the shadows and Starfleet disbands them when people find out they exist.
I expect a very public disbanding may a part of Section 31's plans. Marcus is far too easy with throwing around Section 31's name, even if he did think those he told were never coming back. How does he know they didn't send off an email about it prior to their planned deaths?
But if it disbands there will be speeches full of Roddenberry ideals about not losing what makes us human as we try and preserve humanity blah blah and everyone will pat themselves on the back and Section 31 will continue, more covert than ever.