The Doctor and Dalek Sec do eventually join forces as Sec has lost his Dalek purity and has embraced human emotions. The other members of the Cult of Skaro turn against him because they find out that Sec is un-pure.

Surely it doesn't matter if the Daleks survive or not? as they too can time travel? isn't possible that the Doctor could meet them again in the "past?" Also, again not too sure of the Time frame here I'm sure that the Daleks have visited 1930's New York in "The Chase". Could this be a reference to that story or am I just reading too much into it?

It is in fact a small refrence to the story because when the Doctor uttered ".....Skaro" he didn't sound surprised as he knew he had fought the Daleks here before.