Dear Meenakshi,
The transporatation service which you are providing is not liable to RCM i.e. it is an outward services provided by you on which forward charge applies (not reverse charge) and accordingly you will have to pay necessary GST on total value of the invoice (i.e. sale value of goods + freight).
Further, the tax on inward supplies which you pay under RCM on transporatation services (freight invoice in your name), you can avail input tax credit of the same subject to payment of tax.
Considering above, one is an outward service provided by you to your customer on which you pay tax and other is an inward suppy (though liable under RCM) but you can avail credit of the same against your outward supplies, there is no double taxation.
Regards,
Ronak.