High-Side Current Sensing; I2C
It sounds like you should float a whole circuit at the 3 kV level.  This would probably be something with a small sense resistor and active circuit to amplify the result.  That would be presented to the built-in A/D of a microcontroller, which would regularly report the value serially over a single opto-coupler.  If you really really need it to interface via IIC to the rest of the system, that can be done with a micro on the ground-referenced side that receives the serial stream from the opto and presents itself as a IIC slave.

Keep in mind we're talking about cheap micros here.  The opamp will likely cost more than each micro.

If you don't already have a small power supply referenced to the 3 kV high side, then you'll have to get power to the circuit there somehow.  I know this may sound inelegant at first, but how about batteries?  If this is occasionally run in a research setting, then changing batteries every few months or a year will be less time and money spent than designing and implementing a 3 kV isolated supply, even if this device lasts for a few decades.

If you can't use batteries, then a transformer is probably the best choice.  You will likely have to wind it yourself.  Fortunately, the high side circuit should only need a few 100 mW, so it doesn't have to be all that efficient.  Maybe a suitable toroid potted in high voltage goop.  You can run the primary open loop with a fixed amplitude and frequency square wave.  This gets full-wave rectified, then run thru a small linear regulator to clean it up and make a nice steady voltage.  Again, efficiency shouldn't be a big issue, so you can go for simplicity and robustness.