Okay, this should be interesting.
1. In Tremulous/base, create a directory called "mapconfigs".
2. In server.cfg, add the following line:
set g_mapconfigs "mapconfigs"
3. In Tremulous/base/mapconfigs, create a script called "default.cfg" with these lines:
set g_alienbuildpoints 999999999
set g_humanbuildpoints 999999999
4. Now kill the server and restart it, these changes will then take effect.
P.S. The search button is your friend, learn to use it. -1 karma for making a thread about this when there are already several.