Just to bring a bit of closure, it turns out anticheat wasn't responsible for the FPS drop - the problem happens without anticheat too on a local server, seems like some kind of weird graphics bug in AprQ2 1.20.
I'm experiencing extremely choppy gameplay with r1q2 b6756, only when connected to a server with anticheat enabled.
It's so choppy as to be unplayable. When I tried turning anticheat on and off on the server (and changing maps), the client gameplay would go from smooth to choppy, as the server anticheat went from off to on. It even showed up in the netgraph(!). With anticheat enabled, the choppy client would show a lot more green in its netgraph. But it wasn't server-side lag, because I simultaneously connected an older non-anticheat client (r1q2 b6359) and its gameplay stayed smooth, and its netgraph stayed consistently clean.
My system is Win XP Pro, Athlon 64 3200 (2.01 GHz), 2 GB RAM.
Aha...!!! I don't get the lag if i use ref_gl instead of ref_r1gl !
My r1gl claims to be version 0.1.5.32. OK, I just got 0.1.5.34 from the updater.
OK well.. the choppiness (and visible lag on the netgraph) is still there even with the latest r1gl.

Here are the r1gl settings I use:
set gl_colorbits "" //let r1gl pick the best
set gl_depthbits "" //settings based on the
set gl_alphabits "" //desktop color depth
set gl_stencilbits "" //by leaving these empty
set gl_ext_texture_filter_anisotropic "1" //enable anisotropic filtering
set gl_ext_max_anisotropy "16" //max anisotropy for GF4 is 8
set gl_ext_generate_mipmap "1" //use hardware/driver mipmaps
set gl_ext_multisample "1"
set gl_ext_samples "8"
set gl_ext_nv_multisample_filter_hint "nicest"
Edit: I forgot to mention my video card: GeForce 7800 GT 256 MB (Slightly overclocked / BFG Tech)
Working with r1ch, I've now tried it with gl_ext_multisample and gl_ext_texture_filter_anisotropic both set to zero, but I still get the lag...
Hope this helps,
Regards,
quadz