There's no reason to think that it isn't the same character.
He seems to have a bigger plan that just the same old Hydra vs SHIELD feud.
This happens just as Fitz discovers that there is some other mysterious group who has been messing with the monolith for a long, long time. And at the same time that Rosalind shows up as part of a new group.
My guess is that there has ALWAYS been a group above and beyond the Hydra/SHIELD dynamic...whose members were placed inside those groups to keep tabs (so, Malick was placed in the World Security Council, but possibly NOT Hydra...which is why his name wouldn't be outed as part of the leak).
Personally, I've thought that the show was leading to Zodiac ever since Agent Blake (I think) randomly asked May what her sign is. Agent Carter set up Leviathan, which is a part of the story as well. I wouldn't be surprised if Malick is wanting to recruit Coulson to bring SHIELD back under Zodiac authority...maybe Blake is in on it (we haven't seen him since Deathlok injured, but did not kill, him). You could say that Whitehall was a member and that maybe Malick is trying to talk Ward into bringing Hydra back under Zodiac authority as well.
If you really want to reach...the Zodiac Key could teleport people to its home planet (though otherwise the monolith isn't anything like the key).
Ignore all of this...there's no reason to think it has any truth to it.