I've seen this be ineffective too many times. And your argument could be used for any number of crimes. Making murder illegal did not stop it but it should still be illegal.
Besides, I thought you were taking the libertarian approach? That would seem to suggest that your laws should produce the smallest posssible restriction on behavior in order to accomplish their protective or regulatory goals. If the issue is incestuous reproduction, that should be banned. Indeed that might make it somewhat impractical to get married, but again you're the one drawing the line there, not me.
Handling it this way would allow other supposedly "benign," but strictly speaking incestuous, unions to be allowed. For example, maybe a heterosexual single mother "marries" her own mother, not for sexual purposes at all, but only so that they can gain the legal benefits of marriage and the ability to assist each other mutually in the raising of the child. Where is the state's interest in preventing such a union?
I know these are off-the-wall cases, but basically you're saying that mutual consent is all that matters---except for a marginal health argument. And yet the case for limiting marriage to strictly one man and one woman has socioligical, health, and child development arguments that are far less marginal than that.