If out of the total consideration received by the operator some part is adjusted against receivable from the supplier, should tax be collected at source by the operator even on such amount which is adjusted against other amounts received from the supplier

Yes, as per section 52, irrespective of the mode of recovery of consideration by the supplier from the operator, tax should be collected at source on the net value as defined in section 52(1) of the CGST Act, 2017. There is no deduction envisaged in the CGST Act, 2017 in this regard.

(ICAI FAQ PUBLICATIONS 06-09-2017 TAX PAYMENTS, INTEREST, PENALTIES AND OTHER AMOUNTS: FAQ NO. 57)