I don't get it? The Looms confirm that The Doctor and Susan are biologically related. It's just that Time Lords reproduce differently to us.
Technically yes, but with a twist. In the series, Susan was The Doctor's granddaughter. End of discussion. In the NAs Time Lord's are loomed and don't have children or grandchildren (Because of some curse). Susan is The Other's granddaughter. She is "biologically related" to the Doctor because the Other threw himself into the Looms (For reasons that make little sense) and was re-loomed/re-incarnated as The Doctor. This has the nice effect of making them related, sort of, and making sure that the Doctor never had any of that icky sex with a girl.
"Canon is only important to certain people because they have to cling to their knowledge of the minutiae. Open your mind! Be a Star Trek fan and open your mind and say, 'Where does Star Trek want to take me now'." - Leonard Nimoy