From my understanding there is a by law that forbids beer/alcohol sales with in 1,000 metres or yards of the church.
There seems to be a couple reasons that the variance was not allowed but none mention the fact the restaurant wanted to sell beer.

1) parking or lack of it. Forbidding the variance has not solved this.
Reason restaurant wanted to sell beer was ?? to make more money? and or maybe attract more customers ? which would help make more money is this realistic? but the parking problem remains
Solution might have been to allow variance when restaurant solved parking problem. Without the extra income he/she may not be able to financially do anything about parking problem

2) reaction to restaurant owner not approaching church before applying for variance 
If I was making widgets and determined my customers also wanted to buy gadgets to go with the widgets and it would make me more money AND the Gizmo plant across the road had a by law that no one could make gadgets with in 1,000 metres of their plant I would not want or need to discuss my plans with them.
The procedure is to apply for the variance and post notice so everyone can attend a meeting about the variance and have their say.  There is lots of time allowed after notice in my jurisdiction for people to prepare for the meeting