This is clearly daft. The BBC charter refers to the entirety of BBC programming not to each speparate slot. In a similar manner I would hope any judge invoking the 'Equality' laws would take the BBC's programming as a whole and not apply these (in my opinion misguided) laws to each programme individually.
I think penultimate quote sums my feelings up nicely:
At a debate last week at St Peter's in Marylebone, London, Canon Fraser said the calls for secularists to be included on the slot was akin to putting cricket on Match of the Day.