I am personally not a big fan of team-based colours, especially since when you're in team evil, you would have the wrong colours on the map (red at your base, and blue at the enemy's). But I can understand that differentiating both sides makes it easier for the player and his directions. We'll take your advice on future projects. :)

Then use yellow and purple. Those can be associated with both team-colours.
It's actually just a matter of looking less mirrored than it currently is.

you can write a very very very simple mod that allows you to have red or blue based on good or evil... its really really really easy ;p

in render.cpp

rendergame(bool mainpass)
{
...
loopv(players)
{
...
if(teamskins || m_teammode) team = isteam("good", d->team) ? 1 : 2;
...
}
loopv(ragdolls)
{
...
if(teamskins || m_teammode) team = isteam("good", d->team) ? 1 : 2;
...
}
...
if(isthirdperson() && !followingplayer() && (player1->state!=CS_DEAD || !hidedead))
renderplayer(player1, getplayermodelinfo(player1), (teamskins || m_teammode) ? isteam(player1->team,"good")? 1 : 2 : 0, 1, mainpass);

}
...

void drawhudmodel (...)
{

... //towards the bottom

if((teamskins) && teamhudguns)
concatstring(gunname, isteam(d->team, "good") ? "/blue" : "/red");
...
}

in ctf.h
//in the middle
void rendergame()
{
loopv(flags)
{
...
const char *flagname = m_hold && (!f.owner || lastmillis%1000 team) : f.team)==ctfteamflag("good") ? "flags/blue" : "flags/red";
...
if(m_protect && canaddparticles() && f.owner && insidebase(f, f.owner->feetpos()))
{
particle_flare(pos, f.spawnloc, 0, PART_LIGHTNING, strcmp(f.owner->team, "good") ? 0xFF2222 : 0x2222FF, 1.0f);
if(!flags.inrange(f.owner->lastbase))
{
particle_fireball(pos, 4.8f, PART_EXPLOSION, 250, strcmp(f.owner->team, "good") ? 0x802020 : 0x2020FF, 4.8f);
particle_splash(PART_SPARK, 50, 250, pos, strcmp(f.owner->team, "good") ? 0x802020 : 0x2020FF, 0.24f);
}
}

in capture.h
rendergame()
{
...
loopv(bases)
{
...
regular_particle_flame(PART_FLAME, vec(b.ammopos.x, b.ammopos.y, b.ammopos.z - 4.5f), fradius, fheight, b.owner[0] ? (strcmp(b.owner, "good") ? 0x802020 : 0x2020FF) : 0x208020, 3, 2.0f);
...
if(b.owner[0])
{
...
bool isowner = !strcmp(b.owner, "good");
...
}
else if(b.enemy[0])
{
...
if(strcmp(b.enemy, "good")) { tcolor = 0xFF4B19; mtype = PART_METER; mcolor = 0xFF1932; }
...
}

in scoreboard.cpp
void renderscoreboard(g3d_gui &g, bool firstpass)
{
...
int bgcolor = sg.team && m_teammode ? (isteam("good", sg.team) ? 0x3030C0 : 0xC03030) : 0,
...
const char *icon = sg.team && m_teammode ? (isteam("good", sg.team) ? mdl.blueicon : mdl.redicon) : mdl.ffaicon;
...
}

chasester

or to save on time

here