Okay I am on my way to MQ temple.
And she attacks me, I have no bounty and no saves to back up.
And Whiterun is hostile too, even thought I haven't killed anyone.

You should have paid the fine!!!! Jk but seriously try turning yourself into the whiterun guards that might fix it.

They don't like your kind around that hold.

I fixed it- commit a crime and then paid the fine.

I keep getting this problem in Falkreath even though I don't have a bounty there. Punching one of the guards (immediately surrendering afterwards) seems to fix this for me...at least until I leave and then have to come back there for something. Not an ideal solution, especially if your character isn't a criminal...but mine is.