Amorphous conductor transparent to XRD
You might have success with amorphous carbon sheets[1]. It's not cheap, but it's effective. It's the material used in the windows of the AMPIX cell[2] developed at Argonne. It does react at low potentials, though, so might not work for anode studies.

Have you considered aluminum? It's crystalline, but cubic so there aren't very many peaks to worry about.

This paper[3] might be helpful as you work on your experiments. You're right to think that not having a current collector for part of the electrode would affect the degree of lithiation; it's actually worse than that. Those kapton window cells are convenient, but always put an asterisk next to your results.

I'm doing a fair amount of in-situ characterization for my PhD. If you can share more about you goals, I'd be happy to chime in.

[1] http://www.htw-germany.com/products.php5?lang=en&amp;nav0=3&amp;nav1=6

[2] http://scripts.iucr.org/cgi-bin/paper?S0021889812042720

[3] https://pubs.acs.org/doi/abs/10.1021/acs.jpclett.5b00891