Yes, it's discriminatory.
Child A - attends church - choice of three schools
Child B - doesn't attend church - choice of two schools.
The only difference is the religion and it places Child B at a disadvantage to Child A. Clear religious discrimination.
The issue is that the rules were (rightly) written to protect people the other way i.e. to protect people with a faith from being disadvantaged because of it, and because we're broadly talking Catholic and C of E in a country with still a large population of 'small c' Christians, there's been no real kick back (yet).
It's probably going to take a Muslim/Sikh/Jewish etc family living right next door to a Church school and attending a feeder primary not getting a place and then taking it to court before it will change though, because until then, there's going to be no incentive for the government to even think about taking action.
It's wrong - religions should play no part in state education, beyond a comprehensive overview of them as part of social studies - and the National Curriculum should be just that. National, and taught equally to every child. Every child should be able to have a full education, one not given biases or exclusions because of a set of beliefs they aren't old enough to understand or consent to.