@ Shri Padmanathan Ji & The Querist,
Issue raised by you have multiple facets including who is ultimately bearing taxes, type of taxes paid, risk appetite of the tax payer, implications under income tax & so on. and there can not be any straight-jacket formula.
Kindly allow me to give few pointers:
If one intents to continue paying taxes, it should be under protest by writing suitable letter to jurisdictional officers taking cue of subject HC ruling.
Moreover, continue paying CGST & CGST - while relying on this ruling - is tricky considering the fact that only common conclusion is that, all 3 of them ruled that, CGST & SGST is not payable against such services (although for 3 different reasonings).
Hence, to the extent possible, one should try & get Dept officer to say which taxes should be paid before you continue paying taxes (of course, under protest).
Reason behind paying taxes under protest is to ensure that time-limit of 2 years to claim refund does not deprive tax-payer from claiming refund in case Apex court held that no taxes are payable under GST (which is my view for intermediary services where service-provider is located in India and recipient is located outside India). This becomes absolutely necessary when taxes are borne by the tax-payer from his own pocket.
Another option to be explored is 'provisional assessment' u/s 60 though Dept. may deny it on the ground that subject situation is not about determination 'the value of goods or services or both or determine the rate of tax applicable thereto'.
Last option to be explored is claiming refund of taxes paid till date by the ground that no taxes was actually payable. You can use "suitable portions" from this HC ruling to claim that whatever taxes were paid by the taxpayer was not required to be paid. Depending upon Dept's reason/s for denial of refund-claim (who is most expected course of action), one can explore best course of action going forward.
W.r.t. option of seeking advance ruling, considering past experiences, I do not expect to get verdict agreeing with non-taxability (which is my view). And there is also good chance that they will refuse to give the ruling even though Some HC ruled that such matters are covered for seeking advance ruling. Anyway, I do not see any great value in getting ruling binding tax-payer to pay either IGST or CGST + SGST.
Best course of action - going forward - is dependent of so many factors and same needs case to case analysis to arrive at conclusions. Moreover, suitable changes will be required including agreement/s with customers depending upon course of action chosen going forward (For example: How to avoid bar of unjust enrichment if intention to pay taxes under protest keeping option of claiming its refund in future?).
P.S. Before all above, one needs to first determine if nature of services provided are indeed 'Intermediary' as defied u/s 2 (13) of the IGST Act, with special focus that same does not include a person who supplies such goods or services or both or securities on his own account. If one is not sure that services provided are indeed 'Intermediary', line of corrective action will change dramatically.
These are ex facie views of mine and the same should not be construed as professional advice / suggestion.