1. Guards will comment on you beign dragonborn and saving the land from a great Evil after you kill alduin, its one of the most common guard quips I hear
2. Actually they say psst. I know who you are hail sithis, meaning the know who you are regardless of what you current rank is, it does not imply your some random member.
3. Why would the guards know? seriously its not like the thieves guild told EVERYONE. Its both silly and unreasonable to assume they would know.
4. You are not the leader of the Companions, there is no leader. You arej ust the Harbenger an advisor.
5. Thu'um is a form of magic, knowing it makes you a mage, a rare type of mage but one none the less,
Beyond that you are not forced to join the college for the MQ.
Faction and rank held no weight in Morrowind or Oblivion either besides people saying nicer thigns about.
Try Daggerfall, as Seti18 related to. The faction system there could be tweaked at character creation time, and had =consequences=. If you wanted to, you could set your rep with the underworld to 0 and throw it at the nobles.....meaning you had thieves and assassins after you, while kings would talk to you easily. Or you could just play it; take hit after hit, or steal constantly, and it got harder and harder to talk to the nice folks, as you had the rep of a scumbag. Push that rep low enough, and you couldn't get quests from a certain faction....which required more than one quest giver if it were more than a side quest. That system existed in 1996, and could have been enhanced, debugged, and expanded. Instead it was gutted, and there was no more real consequence in your actions vs. dealing with the population. The X era games may have been getting prettier and prettier, but they have also suffered from FPS-itis. Eye candy over substance....