Yes, you can do that, but it would be better to put the resistor in the return path of the high
voltage supply.
This way, one side of the output is grounded and the other side is only slightly above ground. So, no high voltages are going to get to your expensive micro chip.
HV current.PNG
You will probably need a bigger resistor than 1 ohm and, if the current is very small, even 1000 ohms probably isn't going to make much difference to your current flow.
This will give you a voltage of 1 volt per mA of current being measured, but adjust R to suit your actual current.