Sorry for the delay, @MasterJay! Anyway, answers to your questions:

1.) The Bystanders would only take damage once the Time Stop ends; that's why ArcU used a Time Stop in the first place, so that any Nonpracticing Magi can be pulled out of harm's way once the fight has ended.

2.) Wouldn't it serve Eise better to find the machine projecting the Time Stop and destroy it?