yea I got shunned trying to rescue 2 NCR troops held captive. I messed up and somehow wound up killing all the troops at the ruins. The weird thing is I am shunned from Goodsprings(Im making horrible choices) but can still fast travel to and from there
I don't think your standing with a group is supposed to affect your ability to fast travel to their locations. I am vilified by the Powder Gangers but can still fast travel to the prison. When I have fast travel issues it is that I can't fast travel anywhere,
but I can usually resolve this by changing the zoom level on the map. Once or twice I've had to save and reload my game to fix it.