If the civ ever did get pushed into just the Pakistan/Afghanistan area then it would collapse! This civ must be ahistorical to survive so I don't think a historical (or modern) name will ever really make sense.
I think the bigest problem with Pakistan as the name is Pakistan is a name for the area it is in and the majority of the civ will be out of that area.
You bring up a valid point when you point out that Pakistan is a name only applicable to a small area but I still dont agree with you on not the part of that the civ should not be able to survive. Imo, after the Maratha or British conquer Delhi and most of the Mughal holdings in India, i think it would make sense to let the Empire continue as the Emirate of Afghanistan (which also included most of Pakistan and significant parts of Central Asia as seen from the map below)
Now here is my plan on dynamic names, considering that you add a system similar to that of Linkman's (or just copy his system) where features from SOI are imported; features like Dynastaic Names (for civs like China and Arabia), name change according to territory (for civs like the Moguls and Maratha), and flag and leaderhead changes (communist China, USSR among others)
Dynamic Names:
Ghorid Empire: start out with this.
Delhi Sultanate: Conquest of Delhi.
Mughal Empire: on 1526 ad.
Now for the tricky part:
-If the Mughals survive the British and the Marathas and maintain hemogeny over most of India: the the name stays as the Mughal Empire until empire switches to Democracy or enter the modern era when name will be changed to India (will follow Indian Dynamic names) and the flag will also be changed. I say this because in retrospect if you look at it, it is likely that the Hindus would have asked for greater rights sooner or later if the Empire had managed to survive or the people would have asked for democracy.
-If the Mughals lose India; their capital should change to a city in Afghanistan and they should get a flag and leaderhead change and the following name changes:
Emirate of Afghanistan: the first and default one
Kingdom of Afghanistan: If running monarchy during modern era
Islamic Republic of Afghanistan: Democracy
Democratic Republic of Afghanistan: Communist or vassal of Communist Russia or China
British Vassal: British Afghanistan
Russian Vassal: Russian Afghanistan
American Vassal: Republic of Afghanistan
If Vassal of any other country than no name change.
-If the Mughals collapse; than whenever India declares independence of foreign occupation a separate country emerges as Pakistan (consisting of Pakistan and Afghanistan). If India is already present in the form of the Marathas than independence becomes likely after the discovery of nationalism:
Islamic Republic of Pakistan: Democracy
People's Republic of Pakistan: Communist
Dominion of Pakistan: Vassal of Britain
Protectorate of Pakistan: Default Vassal
If independence is reached before 1850 or the capital is in Afghanistan for some reason (like all other cities are destroyed): then the name become Afghanistan and follows the second system stated above.