I think she felt conflicted because after meeting Palin, she saw how genuinely nice she is. And it was an added bit of guilt that Palin brought her daughter Bristol with her to the set. Remember the nasty digs Tina Fey made about Bristol being "forced" to marry against her will. It must have made Fey feel uncomfortable. In fact, she mentioned being uncomfortable. It's no fun having to meet the person you are "goofing on" and realize that this person is a genuine decent human being who means you no harm and is no fool.
Also, somebody had arranged to have Fey's in-laws meet Palin at a rally. The in-laws are huge Republicans and adored Palin. So, I think the kindness that Palin showed to Fey's extended family also added to the guilt.
Todd Palin signed my Sarah Palin tee shirt at an NRA rally at a southwestern PA gun club in October. What a courteous, personable gentleman. Soft-spoken, thanked the crowd for their support of the McCain/Palin ticket. May the Lord bless and protect that family.