I think you are misinterpreting what the Indian government regulation says. It does not require the carrier to deactivate your account after 90 days of inactivity, it only requires the carrier to not deactivate your account until it has been inactive for 90 days. What happens after 90 days is up to the carrier.
I use Airtel since it is the sole carrier with coverage where I have to visit, but my understanding is that with Vodafone you can keep the SIM alive by just keeping enough of a balance on the account to cover a Rs20/month charge while you are away. This Vodafone web page (see the note after "Step 3") seems to confirm my understanding. Leaving Rs200 in the account when you leave should cover you for a year.
That might not be the absolute cheapest way to keep the SIM alive but it is certainly the easiest and isn't particularly costly.
