The negative contraflexure tends to crack the concrete and because of the continuity, it occurs for a greater length. This is more evident because the deck and concrete are secured to the beams. This distribution of shear connectors tends to be spaced at a greater distance.
Also columns for composite beams often carry up through to support the roof and the beams are 'naturally' interrupted
I've used composite beams continuously without problem, but have staggered the studs on the beam and sawcut down the centre of the beam.
If the slab will be covered with carpet or other flexible topping, just make sure there is adequate reinforcing in the slab over the beam and let it crack away! If appearance is an issue, dik's sawcut detail seems pretty good.
It may end up being less economical. For continuous beams, I would weld siffeners at the beam conn. to each column. Also there are the cap and base plates required at all columns. This cost difference would increase with a greater number of stories. Without any composite action in the negative region, I would double check my beam size and the bracing of the bottom flange.
