Amplifying High Voltage nA Current
You want to measure up to 500 &micro;A with a microcontroller.  A low side current sense resistor seems like the obvious choice unless there are constraints you aren't telling us about.  With 1 kV, it should be acceptable to drop a volt or a few.

Let's say you want 3.0 V at 500 &micro;A.  Do the math.  (3.0 V)/(500 &micro;A) = 6 k&Omega;.  With that between the bottom end of the load and ground, you will get a 0 to 3.0 V signal indicating 0 to 500 &micro;A.

With the large voltage around, I'd put some protection between this 3 V signal and the A/D.  Add some series resistance followed by diode clipping to ground and 3.3 V or something.

With a 12 bit A/D (easy to get nowadays built-into a microcontroller), you get about 122 nA resolution.  If that's not good enough, use a external A/D, like delta-sigma if your bandwidth is low enough.

Added

The placement of the diodes and R4 make no sense in your schematic.

Here is what I described above:



R2 is the current to voltage converter.  It makes 3.0 V at 500 &micro;A.  D1 and D2 clip the result to a safe level, and R1 provides the impedance for them to work against.

One drawback of the clipping is that the impedance of OUT becomes high.  The OUT shown above needs to be buffered before driving a A/D input.  This could be done with a opamp as voltage follower.

Since you end up with a opamp in there anyway, you can consider lowering R2 and using the opamp to amplify.  Whether that makes sense depends on various tradeoffs you haven't told us about.