freight charge in invoice

Your transaction has two supplies
1 Invoice value including freight

No need to pay GST on Freight portion of your Invoice as it will be treated as Composite Supply as per Sec 2 (30).

2. Supply of service from GTA
When you receive the transportation service from GTA you have to pay GST on RCM and take credit of same.

finally option 1 or 2

Your supply is exempted so don't be tax in invoice. And can't RCM applicable on that invoiced freight....

Option 1 is applicable.
Option two is wrong..
Who can make only exempted supplies and they get any URD supplies and Notified RCM supplies they can pay tax under RCM basis...
But, can't take credit....

first of all both are not options.
first supply decide whether you have to pay GST on outward supply and answer is no.

Second supply decide whether you have to pay GST on inward supply subject to reverse charge
and answer is yes you have to pay GST under Sec 9(3).
Let me check how to take "refund" as my entire outward supply is exempt supply as pointed out by Raja P M.

A assessee deal fully exempted supply then he can't take any ITC / Input credit...
So, The above RCM basis payment can't get refund...