Do you think that his nazi in-laws might also have had something to do with it? I know Prince Philip's sisters weren't allowed to attend the wedding and that his side of the family has been kept to the side, even now. It must have been a political sore spot with some of the courtiers and even Queen Elizabeth herself, as she was known for detesting Germans in general ever since her brother was killed in WWI.
Of course, I know that Prince Philip was always against the nazis and served with distinction in the Royal Navy during WWII, so I am not questioning his loyalty at all. I believe the reason Philip took his mother's family name rather than his father's was to downplay the German connection of all of his sisters being married to Germans and at least one to a prominent SS officer, Prince Christoph of Hesse, who served as an intelligence officer to Goring, as an aide to Himmler, etc. Thankfully, he died during the war or that might have made the marriage between Philip and Elizabeth even more politically sensitive.
Thank goodness they did persevere and marry; they're a wonderful example of what true love really entails; devotion, sacrifice, and putting the partner's needs in front of one's own.