Well I've heard that the Seventh Doctor is the darkest and, in a way, he is. Keep in mind, though, that is Remembrance of the Daleks The Doctor had few choices.
1.) Take the planet-destroying device with him in the TARDIS and risk the Daleks getting it someday.
2.) Try and destroy it or make it useless, risking the Daleks fixing it someday.
3.) Turn the device into what basically amounts to a bomb that will explode as soon as the Daleks try to use it.
Also keep in mind that, while the Doctor may be against killing an entire species, when it comes to the Daleks and when it comes to the Daleks getting a device that they WILL DEFINITELY USE to try and destroy all other life, he makes an exception (like he did during the Time War). Hell, he even WARNS the Daleks, one last time, that they should not use the device (albeit in the angriest way possible).
Now, keep in mind, though, that I've only seen Remembrance of the Daleks and if the Seventh Doctor does this with every alien species (when he has another alternative) then I can see why people wouldn't like him.
But, hey, why can't one version of the Doctor be more serious?