The reason that Target does not allow charity's at their doors has to do with their solicitation policy. Target gives to the Salvation Army and many other community charities. I am not sure if you are aware but Target gives over 3million a week to charities.
Target is very guest service oriented and are aware that a lot of people do not feel comfortable when people ask for money or they don't feel comfortable stating that they do not have the money to donate. So to avoid that, no solicitors.
As far at the reference to Christmas, They have Happy Holidays--why not try to tailor the message to everyone that has a holiday instead of just tailoring the message to those who celebrate x-mas?