In my experience, once Alexa has found a hue bridge there is nothing you can do to stop her from adding those devices on that bridge back to her list after a discovery is run. Even if you delete them from the Alexa app or website. Alexa also doesn't remove a device automatically if you've removed it from being discoverable. You will need to remove the device from both the Alexa app, as well as the Echo App for it to be completely removed, otherwise another discovery will bring it back to life.
The new Alexa Skill will have some built in options to help alleviate some of these issues. Still no firm release date, but the Alexa skill is very close to being finished, and now has the ability to actually lock/unlock/arm/disarm via PIN code! They just released this long awaited feature and it will be supported by our Official Alexa Skill.