Re: Secular?
I do not think the comparison is the issue here. 
If Pakistan had roits, that does not mean India did not.
Moreover, neither the outward migration (efflux) is a measure of any country to be a bad country, nor Pakistan showed any acceptance of muslms fom India during those days.
To elaborate more, migration might not have happened due to fear of repurcussion on other family members, or not having means to migrate. Other factor may be that those muslims moved to a third country if they had the means available.