GST is applicable in this case. The commission is earned on supply of service (agency service). The rate of tax will be 18% and you can take input credit.
If you agent is not registered then you have to pay tax under RCM post March 2018.
If you are giving discount in goods and it is part of an agreement with your agent, then you can issue a credit note and reverse GST on it.
If you are giving discount without a prior agreement then GST reversal is not possible.