In my book this is a non-issue at even a semi-decent level of play. Auto piloting is a general problem and not one specific to stun/silences, people just need to get good and know when they need to save their silence/stun abilities for special enemy skills and when they can use them on cd as a dps increase. Pointing out the fact that these abilities can be used as a dps boost when their secondary effects aren't needed as a bad thing is not the correct approach imo, just learn the correct utilization.
