I don’t know if Instamojo has resolved this multisite issue, but I have moved on to razorpay and it is much better.
Since Instamojo support is so lacking for a prolonged period to address simple integration issues, it is probably best if you too looked at the plenty of other choices available.
The callousness of Instamojo’s team can be understood from the fact that they have not bothered to monitor this support space nor answer any queries satisfactorily.
All the best.