You can use CancelInvoke where necessary, but it sounds like coroutines would be more appropriate for this than InvokeRepeating.

private var addingResource : boolean;

function Loop () {
    while (true) {
        yield SpawnNewCharacter(4.0);
        yield AddResource(4.0);
    }
}

function SpawnNewCharacter (delay : float) {
    while (!addingResource) {
        Instantiate(character); 
        yield WaitForSeconds(delay);
    }
}

function AddResource (delay : float) {
    while (addingResource) {
        resources++;    
        yield WaitForSeconds(delay);
    }
}

In this case, setting "addingResource" to true or false toggles between the two functions.

http://unity3d.com/support/documentation/ScriptReference/MonoBehaviour.CancelInvoke.html Seems like you could do that easy enough