[...] Marcus wasn't acting under Starfleet's orders.
Well, he was the head
of Starfleet, so who exactly in Starfleet would have been giving him orders anyways?
Yeah, but as the head of a military you don't simply dictate how that military works. A military serves under the ruler(s) of a nation. So even as head of Starfleet, he wasn't the Supreme Ruler of the UFP or something like that, and couldn't dictate policy.