The study referenced in this article is here: Sexual imprinting on opposite-sex parents. (Published Sept. 2, 2008 by Tamas Bereczkei at the University of Pecs in Hungary in Proceedings of the Royal Society B, just as the Guardian says.)
While the study did conclude that "Significant correlations have been found between the young men and their
partner’s father (but not his mother), especially on facial proportions belonging to the central area of the face", if you scroll down to the last page, you will find a Retraction notice:
After careful examination of the above paper, published in
Proceedings of Royal Society B: Biological Sciences
, we have
realized that we made a number of serious errors. These errors relate to the numbers of families included and several
erroneous values in the tables. This failure led, among others, to an extremely high correlation between the male subjects’
mates and subjects’ parents in the facial proportion jaw width/face width. Furthermore, we have chosen a relatively simple
statistical process of randomization, instead of using a random sampling permutation method. Therefore, we wish to
retract our published manuscript.
Of course, this does not disprove the thesis itself, but the research referenced in the article you found turns out to not be significant.