I think their are a couple of issues with using Sisters of Battle as being the way of haivng a female character. Aside from the limitation of choices it leaves that player, it also creates a situation that flies a bit in the face of the roleplay. Every game a scenario would have to be concocted to give an explanation for why a single individual Sister of Battle is running along side the toughest most veteran of alien hunting space marines. While there is an overlap of threats between what the Deathwatch and Sisters of Battle seak out, each originate from different Ordos of the Inquisition and tend to avoid interaction. You have to consider each as almost being like the SWAT teams of the CIA and FBI; they'll only ever work together if forced by a higher authority. For anything other than a one off game it would become convoluted to explain why such combined action is required.
I don't like enlsaving a campaign to a settings details, latitudes to invent are important for personalizing; its just when you go too far you may be playing the game in name but not in spirit. It is almost as much a "sin" to allow something that doesn't fit as it to disallow something that does. If we were playing old school D&D and you were only allowed to play a human character, what would be the point. So if you play a game that focuses on a particular faction or force within the 40k setting, what is the point in not playing that faction.
I like the idea of putting something on the table to make female characters I just don't belive SoB are the best option. I think the two ideas that have been voiced that I'd push are either a high level assassin or a female Ordo Xenos Inquisitor. Both of those create the opportunity not only for the player to roleplay female but the oppurtunity to have a character that emphasizes abilities that Deathwatch lack. Then it just becomes a matter of giving the player enough start experiance to balance them as well as necessary.