Well, never heared about google :) ?
Look at game-deception it explains how to modificate a qvm (' after it has been compiled '). It just over-compile the certain lines / commands. The only problem ( for you ) is, that you have to work with opcodes ( / assembler ). Well, here's the tutorial made by the great macpunk : http://www.gamedeception.net/threads/19198-Runtime-QVM-Modification
vmHeader_t *hook_VM_LoadQVM( vm_t *vm, qboolean alloc )
vmHeader_t *ret = orig_VM_LoadQVM(vm, alloc);
vm->instructionPointers[0x0FF5E7] = 0x00; //0x00 is the opcode of whatever you want the instruction to be
You need to Quake3 Engine SDK for the structs.