I think Rose makes the same point to the Doctor in this episode, and his response is something like 'yeah, but I know what I'm doing'. Or something.
Although it's never been clearly stated, I think the Doctor knows when he's supposed to be part of events and when he's not supposed to interfere.
There are a couple of clear pointers from the Peter Davison era (Earthshock/end of the dinosaurs and The Visitation/great fire of London).
But the best example is from Pyramids of Mars when the Doctor (Tom Baker) lands in the early part of the 20th century. He realises something is up (alien plot to destroy the earth) but Sarah Jane asks why they don't just return to the present as they know the Earth wasn't destroyed in 1912 (or whenever) as it isn 't part of history.
But the Doctor says they have to get involved, and to show her why he returns them to Sarah's present day earth only to find it completely destroyed - history was changed because the Doctor didn't get involved.
Anyway, they return to the past, defeat the baddy and everything is as it should be.
Which is a big, roundabout way of saying that the Doctor, through his travels - and I suppose his Time Lord 'time sense' or something - simply knows when he should be interferring (when he has become part of events) and when he should leave well alone.