It won't be a waste of time, it will be time spent getting to Entity, just like normal.
They are still dropping Phials, maybe receptacles, and still giving good AA xp. This isn't nothing.
That would just hurt the people who are doing things 100% legitimately. Sometimes people crash at end of fights, or you have dead people that need revived. If FC wanted to go the route of stopping relogs, it would be better to bind people to the box when it spawns, not when it dies.
It wouldn't be all that horrible, since half the good loot is now on Emp + Zodiac. And you aren't going to have any random pug easily be able to do Entity Phase 1. Even Entity Phase 2 isn't a walk in the park like T1/T2 raids.
Next up, time to nerf the heck out of priests so they can't heal and dps at the same time.