Really it comes down to the writers not knowing how to stay true to what the Federation should be, and not knowing exactly how to show someone leading without also coming off a bit like a tyrant. They really tried to express her command which is why she comes off arrogant and tyrannical at times, however, the situation does call for it, and most captains we have seen do similar acts. So it fits in the universe, and the issues come more from what we all would want in a show, and want the federation to really be, than what those things really are.