Most of the area is rural. Unguided ballistic missiles will end up in some field or forest and kill some cows and deers.
First, let me clear the cruise missile part-
Babur is waste not becayse of BMD but because of SAM and BVRAAM. All subsonic cruise missiles are far inferior to an aeroplane which can travel at over 1Mach speed and can maneuver much more than a cruise missile. If a SAM can take out a plane, it can take out Babur with 5 times the ease. India had SAMs like Akash, BARAK-8, QRSAM and also has BVRAAM ASTRA to take out subsonic missiles like a plane takes down another plane.
Now, about Ballistic Missile -
Lets take a scenario- Pakistan launches 100 BM from lahore towards Delhi. India immediately detects the launch and before the missiles reach India, a massive counter attack will be launched.
Next, people will be asked to go inside heavy concrete houses or buildings in the city to reduce damage. And jammers to jam the satellite signals of GPS, Beidou, Glonass and Galileo will be deployed extensively. Since Pakistan doesn't have access to military grade location and guidance system due to lack of satellite constellation, it won't be able to guide its missile in a jamproof manner
Next, the missile won't be intercepted in launch stage as there is too little time. But, India will then try to intercept in exo-atmosphere with theatre defence systems. Few will be destroyed while most will continue.
Finally, point defence BMD systems to attack the incoming missiles at reentry stage will be fired. The probability of success for short range missiles under 500km will be over 75% due to slower speed. But, for MRBM, it is about 50% or less. Generally, a BMD launcher can launch 4-5 missiles. Depending on the number of launchers available, the ratio of ABM to BM can vary. A large number of warheads will be neutralised while some will strike the targets.
Due to precautions taken of getting people inside the house, jamming the guidance and destroying over half the warheads, the damage is significantly reduced. On the other hand, immediate detection of launch and retaliation, Pakistan won't be able to fire a second wave.
Next, it comes down to who can withstand the damage of the first wave strike and still continue. This depends on technology levels to mass produce equipment to cover the losses and most importantly, food supply (India is food grain surplus and area under other crops like sugarcane, cotton, banana etc can be diverted into food grain production). So on....