Pulsed DC current measurement using arduino and shunt resistor
You need to have a reference potential somewhere, anyway. If the source is grounded, than you already have it. If it's floating, then you may attach a ground like you did.

In case a source already has a connection to ground, then you have to pay attention on max. common mode voltage of difference amlpifier. The schematisc is not very clear, a clearer view of the difference amp. would help.