Wide range current sensing at +5kVDC
Does this sort of architecture seem sensible?

No.  You are trying to pass a high dynamic range analog signal over optical isolation.  That can be done successfully for some value of "success", but you are very unlikely to get the accuracy and repeatability you want.

I would make a small isolated power supply, probably using the flyback method with a small transformer rated for your voltage.  A few 10s of mA at 3.3 V is all you need.  Depending on your situation, maybe using a couple of AA batteries is appropriate.

This isolated circuitry looks at the voltage across a sense resistor, converts it to digital, then sends the digital information over a opto-coupler.

You haven't said anything about accuracy or response time, although you do have a large dynamic range.  Use a delta-sigma A/D to convert the voltage on the sense resistor.  That gives you the large dynamic range you need.  It might take 20 ms per conversion, but this doesn't conflict with any specs you have provided.  If the ultimate goal is only to display the value to humans somehow, then this is still way faster than needed.

You add a little low pass filtering in front of the A/D.  Note that a sigma-delta A/D inherently filters also.  Run it as fast as you can anyway, then do some additional low pass filtering digitally.  The result can be used to update a display every 500 ms or so, or move a needle with maybe about the same time constant.