Use "seta" only if you wish it saved for future. If you want it set for the current session then use "set" ("a" - archive, archived in server.cfg). And direct assigning should be done anyways so avoid "set[a]". Like "rcon g_gravity value" via rcon or if you have access to the game console, just "g_gravity value".
The cvar is actually read only in MBII but I browsed the code a bit and there seem to be an other way to set gravity using some level vars. I will be able to check it fully tomorrow and tell you. Or maybe some white knight appears and help before.