The mini-episode, broadcast during the Comic Relief telethon, continued Whitney's sexual exploitation plot and saw the vulnerable teenager, played by Shona McGarty, escape the clutches of Rob (Jody Latham).
However, confirming that some viewers thought that the material had been "inappropriate for a family audience", the BBC acknowledged that it was a "challenging storyline", but insisted that it was "in line with the show's long tradition of tackling difficult social issues".
"The EastEnders audience would have been aware of the dark situation Whitney was getting into. In the preceding episodes viewers saw Whitney feeling increasingly unwanted and unloved, with her brother and her step-mother absent, her life was taking a downward spiral," the official response stated. "Alone and unhappy, she fell for the charms of an unscrupulous man, Rob, who began to manipulate her and ultimately exploit her sexually for his own financial gain.
"We have been working with experts and charities funded by Comic Relief in order to research this story - which explores a growing problem facing many young women in the UK today - and to ensure it was told accurately and sensitively."
The corporation reiterated that the hard-hitting plot had been researched thoroughly and that a number of charities had been approached, who confirmed that they "are hearing stories like Whitney's more and more often".
The statement continued: "It was a natural progression of Whitney's story thus far and we felt it was an important story to tell, and hopefully to raise awareness of amongst our audience. In doing so, we believe it was right to show the - albeit unpleasant - reality of the situation faced by these girls, rather than put a gloss on it.
"In the episode Whitney is seen to escape and to raise the alarm - we did not leave the audience on a cliffhanger. The menace and danger Whitney is in whilst clear is implied rather than graphic or sensationalised and is in keeping with the audience expectations of how EastEnders would tackle a tough story in a pre-watershed manner and indeed how Whitney's story has evolved over the last few years."
Directly commenting on the episode's scheduling during the telethon, the BBC said: "We are conscious that Red Nose Day programming includes many different tones and themes, ranging from light comedy sketches to difficult and emotional appeal films, all of which played out around the time the EastEnders episode was scheduled to transmit."
It continued to add that presenter Davina McCall had highlighted that Whitney appeared in "real trouble" and that the "tone and content" of the episode was "clearly sign-posted to viewers".
"We hope that the majority of the audience would have heard the first extended warning and that the serious tone of the introduction, though truncated, pointed to the fact that the upcoming film was a gear change. It was further put into context by the presenters at the end of the piece, when they talked about the Comic Relief-funded charities working to help girls like Whitney," the statement concluded.
Comic Relief's head of UK grants Gilly Green previously praised the Albert Square soap for "profiling this issue".
> Jody Latham wept over 'Enders research