We know that the defacto ruler of whiterun is this high priestess witch thing, and is the head of this, "whiterun coven of witches" but what exactly does this mean? is this another joinable faction/guild? a more evil alternative for the magic user than say, the college of winterhold? do you have to be female to join? has anyone heard anything about this?

They are described in the lore, but we don't know if they will make an appearance in the game or not.

in the lore a they more of an evil faction?

Not really specified
However they worship Shor/Lorkhan so are likely to be opposed to Alduin

Ok so earlier i mentioned the Whiterun Witches Coven with several questions about whether or not it was going to be a joinable faction, or whether or not it's going to be a more "evil" alternative to the college of winterhold. i cant confirm yet whether or not it's an evil faction, but its existence is confirmed within the x-box 360 achievment list. look for the one called "blood oath"
http://www.xbox360achievements.org/game/elder-scrolls-v/achievements/

That achievement mentions "The Circle". Nothing about the Witches.

i actually hope its an elite den of fighters and i believe they confirmed only 4 factions so probs not joinable but quest related

For more on the lore, go here: http://www.uesp.net/wiki/Lore:Whiterun

Be sure to click the links in the articles.

Still part of the Companions questline...

Hopefully the Companions quest line will be much better than the Fighters Guild quest line, which it seems like it will be!

a fight club perhaps?

Thanks for the link Echo ^^

Don't forget this was around the time of Oblivion, not Skyrim.

Things might have changed.