Do not get into the tax net, or you'll never get out of it.
The 0.4% transaction tax is on transactions bigger than Rs.50,000. So just don't make transactions bigger than Rs.50,000.
You qualify as a self employed (Non-Salaried) person. If you don't hide your money, you might end up receiving a notice soon.
Tax on 1 lac per month (1.2 million per year) will be :
Rs.102,500 OR Rs.8,542 per month.
You don't get tax certificate from employer (That is proof that the company has deducted tax on your salary and already paid it to FBR). You just get yourself an NTN and file a tax return (which is basically self assessment).
Also, since your business is free lancing and is "portable", try to simply shift it abroad. Register your business in a tax free country.
There are so many.
Also, software export income is not taxable if I remember correctly. I don't know whether it is only for companies (no corporate tax) or also on personal income. You need a tax consultant/attorney.