Even if you use whatsapp on a $50 phone (which you use for say 5 years) with a $3/month plan (which seems incredibly cheap), you have amortised costs of $46 per year. Increasing it to $47 to get whatsapp does not seem as unreasonable as you suggest.
Malawi is also an _extremely_ poor country, for reference Bangladesh have ≈ 5% smartphone usage with a GDP of ≈ 4000 USD per capita (PPP) while the GDP of Malawi is ≈ 1000 USD (PPP) per capita.
I would argue that not paying (but having the means to actually use whatsapp!) is more of a choice, or lack of payment infrastructure, rather than not having the disposable income to spend 1 USD per year for the service.
If India and Malawi and whatever other country can't pay for WhatsApp, they don't get it or Facebook makes it free just for them. Or they find a way to make the ones that can pay do so.
What's the big deal?