OK, firstly realise that modding the .dlls is not necessarily trivial. They are stored in assets3.pk3 (if you have patched), but you will need to recompile (possibly just jampgamex86.dll), and put in your mod directory.
It would be easier if you have MS Visual C++ 7, or at least MSVC6.
This (
http://www.lucasfiles.com/index.php?s=&action=file&id=331) is the SDK you need. (IIRC there is also a modelling SDK).
Unzip it, go into the codemp directory it creates. Read the MakeAMod_readme.txt (not very helpful I'm afraid). The best intro I've read for Quake 3 engine modding is Code3Arena (
http://www.planetquake.com/code3arena/index.shtml). Be aware though that JK:JA does not use QVMs, for reasons best known to Raven it uses .dll files for Windows and .so files for Linux.
Open up the project file in MSVC7, if you have MSVC6 there is a project converter here (
http://www.arstdesign.com/articles/prjconverter.html) or here (
http://www.codeproject.com/tools/prjconverter.asp) .
Open up g_weapon.c, find the function WP_DisruptorAltFire, and see why the disruptor disintegrates the target.
This seems to be the code:
if (traceEnt->client && preHealth > 0 && traceEnt->health <= 0 && fullCharge &&
G_CanDisruptify(traceEnt))
{ //was killed by a fully charged sniper shot, so disintegrate
VectorCopy(preAng, traceEnt->client->ps.viewangles);
traceEnt->client->ps.eFlags |= EF_DISINTEGRATION;
VectorCopy(tr.endpos, traceEnt->client->ps.lastHitLoc);
traceEnt->client->ps.legsAnim = preLegs;
traceEnt->client->ps.torsoAnim = preTorso;
traceEnt->r.contents = 0;
VectorClear(traceEnt->client->ps.velocity);
}
Include something similar in the right place in w_saber.c and rebuild the .dll
You may need to add more code to get it to work, but I'll leave that to you :)