What, are you saying we should define the constant c to be the speed that light actually travels through space, rather than the speed it takes through a theoretical pure vacuum? That would be silly, because for one thing the constant c has other meanings besides just being the speed of light through a vacuum. In fact, you could argue that it makes more sense to define it as the unique invariant speed required by the theory of relativity, and that definition is not affected by the presence of matter.
Also, what if you were in a patch of space with a lower density of matter? Intergalactic space, for example? Would you have to raise the speed of light to compensate for the lower density? The appeal of the fundamental constant c is that it's universal, it takes the same value everywhere, regardless of local conditions.
Also, even in the space surrounding the Earth (once you get far enough up, a few hundred km), the density is so low that if you shine a laser in some direction, most of the photons in that laser beam will travel 300,000 km and more without ever hitting a molecule.
Also, what's so special about 300,000 km anyway? You could shine a laser half a mile and measure the time it takes.
And - I really should have thought of this before - getting light to travel a given distance and timing it is not even the best way to measure its speed. You can actually do it better with an interferometer, which is a device that splits a light beam into two, sends them down different paths, and recombines them at a receiving screen. What you wind up seeing is a set of "fringes" which shift position as the length difference between the two paths changes, and the exact rate at which they shift position depends on the speed of light. So you can measure the shift and use it to calculate the speed.