Master Chief is certainly not a female. The video you are talking about is a fan made video and the guy thought it would be cool if he made Samus fight a Spartan that turns out to be a female (the one from DOA). As I understand, Master Chief is a male in the books, and the guys responsible for the storyline have said they have tied everything together, the books and games, so that nothing contradicts for those that enjoy both.
As a matter of fact, Gamersyde did an interview with two guys from Bungie, and you can read it here: http://gamersyde.com/news_4786_en.html
Edit: By the way, those wanting to see the "Haloid" video and read about the creator and his thoughts around why he made it, go here: http://www.gametrailers.com/umwatcher.php?id=57998
Threads of Interest:
The Movie Thread: http://www.vgchartz.com/forum/thread.php?id=6880
The Crow Eating Thread: http://www.vgchartz.com/forum/thread.php?start=0&id=3886
The Betting Thread: http://www.vgchartz.com/forum/thread.php?start=0&id=7104
Custom GIFs Thread: http://www.vgchartz.com/forum/thread.php?id=18963
The Greatest Game Ever Conceived On Any Platform
Tag: "I have tasted Obi-Wan's bitter tears"
