Welcome to the site! <img src="i/expressions/face-icon-small-smile.gif" border="0"> This is a great place to come for support and information as you continue to learn about CF and the many complexities involved in caring for a child w/ the condition. I'm so sorry she's had such a difficult time of it lately. Everyone above is right in that it's important to avoid as much illness and germ exposure as possible, esp when getting over a recent illness or during an otherwise vulnerable time. You aren't being paranoid in wanting to protect her from further illness and being as informed as possible about risk and how to avoid it is important in helping to avoid disease prevention.
However, there are circumstances involved in this situation making it important to tread a bit more lightly than in many other 'sick family or friends' situations where we would simply put our foot down and say 'you need to stay away from our child if you are sick.' These are his children and he has a responsibility to him, legally and most importantly because it's the RIGHT thing to do. I wouldn't want anyone here to forget that. Having them with him during his scheduled time is not/should not be 'optional', even when they are sick (it's part of parenting, after all.)
If you don't live with him, it should be pretty easy to keep your child away from your boyfriend's children if they are sick- after having a good discussion with him re. the dangers of her getting sick again, etc. No one can force you to go to his house or to let him come to yours. However, if you DO live with him, it's going to be more complicated. He cannot default on the responsibility he has towards his children in favor of a new relationship, in my opinion. However, a discussion still has to be had on how to minimize risk to your cousin and precautions that can be taken to keep to limit contact with each other, etc.
I hope nothing I said offends anyone; but I just wanted to present an alternate view.