Against a maneuvering missile?
What missile starts evasive manoeuvres 100km from target?
Besides, 100km against a missile is pretty unrealistic to start with given the detection difficulties.
Rail/gaus gun CIWS really comes into their own on the 5-25km range category.
Missiles will still be flying in cruise mode at such ranges, so will be flying nice predicatable flightpaths, so will be much easier to target compare to those missiles in terminal mode, where they are doing evasive and/or boosting to supersonic speeds.
The accuracy rate will be further boosted by the high speed of the projectile.
In effect, with rail/gaus guns, you can vastly extend the effective range of your CIWS to medium range missile territory.
There is nothing stopping you keeping FL2000s and laser gun based CIWS as well.
So rather than seeing them as a straight swap for traditional or laser CIWS, see them as an added bonus layer of defence.