I can only hazard a guess, not having been privy to their decision myself, but I would wager it was first because mages are natives of this world well-known to the Inquisition. They have a long history here, and know that they will have to live with the consequences of their actions, and that those mages that come after them will suffer for their choices as well. Whereas rifters come and go at random, and may hope they will soon escape their fate. Second, because when the issue arose, mages quite incredibly followed orders to deliver the phylacteries back to the Inquisition despite their misgivings, then calmly organized and pursued the matter through official channels and peaceful action, without--to my astonishment, I will freely admit--a single threat of violence.

Whereas your fellow Rifters, whose histories, motives and capabilities are largely unknown to us, have immediately responded with public temper tantrums, property damage, threats of violence, and calls to abandon the Inquisition altogether and hare off across Thedas. It does not precisely inspire the same confidence.