I think the decision lies on your pocket.
Anti-CNG guys would say 'dont destroy ur car'...but the fact is they dont fill ur pockets.
If you have 50-60k Rs ready for investment then you can recover most of it when you sell ur car.
Even with hiked CNG prices, the cost/km on CNG is almost half as that on petrol. For 80 km per day...I think you will save A LOT of money every month. Plus when CNG is not available or when you see long queues you can also drive on petrol.
You have a nice economical car, going more economical is always sensible. Drilling two holes in the trunk wont destroy ur car. Lets accept Its just a Honda City after all, not a Ferrari that you wont like any one touch it.