For one thing, it wasn't a very deep thought that caused him to wish for her to still be alive. Instead, according to here:
Upon her death, Yuuko finally explains her connections with Clow Reed. As Yuuko lay dying, Clow Reed had the briefest thought that he wanted her to remain alive. Clow's magic was so powerful that this single thought caused Yuuko to become frozen in time.
Additionally, according to here:
In Tsubasa: RESERVoir CHRoNiCLE, Clow Reed is mentioned by Yuko frequently. They seem to have worked together for the same event that Yuko always talks about: "the day that has to come". For this purpose, both created the Mokonas (which implies that they had met the "Real" Mokona of Cephiro).
As far as I can tell from everything I've read, they are not related by blood. Instead, they worked together. They may have been no more than acquaintances or maybe friends, as there seem to be few implications that they were ever anything more.
The only time I have seen it implied was in Chapter 138 of Tsubasa, where Clow said to Sakura, "Being apart from the one you like, no matter how old you are, is a lonely thing. And while apart, I'm wishing for that person to be happy." There are thoughts that he may have been talking about Yuuko. It is possible that he was talking about Madoushi, but Madoushi only appeared in an anime movie and so may not have been canon to the manga.
I cannot find any official statements on the matter, though.