Yeah, but claiming that RTD-era Who deifies the Doctor is a bit like claiming that The Gospel According to St. John depicts Jesus as just a human being. It's a clear contradiction of the actual, incredibly obvious, message.
I think the message you speak of is only "obvious" in
Waters of Mars.
No, it's obvious in quite a few episodes -- in "Dalek," in "The Doctor Dances," in "Boom Town," in "Bad Wolf," in "The Parting of the Ways," in "School Reunion," in "The Runaway Bride," in "Gridlock," in "Human Nature"/"The Family of Blood," in "The Sound of Drums," in "The Fires of Pompeii," in "Midnight," in "Journey's End," in "The Waters of Mars," in "The End of Time, Part Two." In all of these episodes, the Doctor makes morally ambiguous choices that the episode is not clearly endorsing, or he makes a major mistake, or he behaves in a selfish manner, or he becomes extremely emotionally vulnerable, or he generally behaves like an asshole.
The Sound of Drums, however, has Martha convince the human race to believe in The Doctor, place their faith in him and pray to him like a deity, so that he might defeat evil and save them.
No, it has Martha telling people who the Doctor is and then telepathically channeling their own psychic energy to him, allowing him to channel humanity's own psychic energy into defeating the Master. The Doctor is just humanity's vessel -- that's why he specifically cites the greatness of humanity as he defeats the Master.