I believe this is more of a Risk Management problem.
Firstly, as a CEO (Assuming he is an Indian) would already be aware of the political instability between the two countries.
Secondly, there are plenty of strategies that could be employed,
1. Diversify the business to countries with similar demand for your products. (Possibly Afghanistan)
2. If you are getting into Afghanistan, you could explore the possibilities of importing your goods into Pakistan via the Afghan border through your entity registered in Afghanistan. Of-course the commercial and legal aspects would need to be evaluated. However, a lot would depend on the profit margins you get from your exports to Pakistan and the impact of denting your margins in your biggest export market on other international businesses.