First of all interceptor missile is one of the choices, that doesn't means that they will be fired always when they saw an incoming missile. You can cross check it. The yemane rebels fired two missiles on USN few months back, no anti ship missiles were fired all are deflected electronically. As you said brahmos can electronically generate clone of brahmos along with original missile, same thing can be done with ships too, i heard this capability when we have inducted our very first ship from talwar class frigate family, the INS talwar.And if we are firing missile to intercept incoming missiles at long range you have to assume that ecm technique are not choosen. And for close range interception, interceptor missiles will be using either mmr radar or IR homing, at the same time most of the antiship seekers are in xband, so you can effectively try to jam incoming missile without jaming short range interceptor missile.
Even if both having same frequency band, you can jam incoming missile without jaming interceptors, how aircrafts firing missiles & jaming enemy aircraft? It may be difficult but possible.
What i feel is that, Brahmos is a very potent platform, but its not invincible. It can be dodged electronically if enemy found its launch much early and its highly likely too. At present day threat scenario, we need to develop next generation antiship missiles like NSM of Norway.