Ethnic minorities and diasporas have seldom come in the way of the aspirations of mainland communities. We have so many examples in history. There are as many Muslims in India (if not more) as in Pakistan but Pakistan came into being on the basis of a separate homeland for Mulims. Why not look at China (Chinese all the way upto Indonesia), Russia (Russian minorities throughout Central Asia), Tajakistan (Uzbaks), Uzbakistan (Tashkand is primarily a Tajak city), etc.
Actually if you look at the creation of Pakistan, it was an ethno-religious endeavor instead of purely religious one. The far Northwest and the Bengal East were considered to be areas of high Muslim concentration. No one expected Kerala's Muslims to be split and join Pakistan. Regardless you can not deny the massive (one of the largest) human migrations in the history occurred with the partition. Also there are not as many nor were there ever as many Muslims in India as Pakistan. Before '71 East + West Pakistan far exceeded the # of Muslims in India and afterwards, Pakistan continued to hold a slim lead over Indian Muslims (which has been widening).
Lets talk China: Are aware of their hated status in Indonesia, Malaysia and other countries where the diaspora exists? Outright discrimination, ethnic violence and state sponsored anti-Chinese policies are the norm. They may exist but they are barely tolerated.
Russian minorities are clearly not well integrated except for places liek Kazakhistan. This also has to do with Russia being the "dominant" nation in teh region. A Pakhtun-Baluch state would hardly be "dominant" enough to protect its minorities in the rump of Pakistan. Sindhis+Punjabis+Urdu Speakers would outnumber us at least 4:1. Even if Afghanistan + Baluchistan va Seistan are throwm in the mix, there is no comparison. The Punjabi nation alone would exceed those numbers.
**
Yugoslavia itself is an example. There are serbs in Bosnia-Herzgovia, Bosnian Muslims in Serbia, Croatians in Serbia, Serbians in Croatia, etc.**
That is a great example of bloodshed. Bosnia having thousands of Muslims, Croats butchered (even now, Bosnia is barely one nation), Muslims in Serbia = Kosovo, Croatians in Serbia are miniscule, and the same goes for Serbians in Croatia. Basically the Yugoslav Muslims and Croats were both victims of Serbian massacres and displacement. The break up of Yugoslavia was a horrible mistake where these smaller formerly peaceful groups broke out in warring factions and massive conflicts that threatened the entire region. In no way was this a "positive" experience for the Croats, Muslims, and Serbs. Maybe the Slovenes came out well.
In these circumstances, UN charter, international norms, and state responsibility come in play to protect minorities.
I would rather give up my dignity than to allow the UN charter, international norms to ensure the safety of my ethnic kin. There is no way Pakhtuns in Karachi would be safe under any Pakistani state, same would apply to Baluchis in Sind and Punjab. That is not a gamble that I or any rational person is willing to take. After the proven experiences of the India-Pakistan partition.
The best bet for Pakistan is autonomy as devised by the Lahore Declaration and reaffirmed by the 1973 Constitution where the Centre must devolve the power to the privincial level, with concurrent rights and responsibilities within the Federation. For too long, Pakistan has been politically dominated by the pronvincial elites of Sindh and Punjab with the Western provinces playing an acillary role - this must change.