Jetpacks are an inherent part of the game. The map's "flow", or pathing, did not originally have a state in which the jetpacks don't exist in the shipping game. They even mentioned making adjustments to Reflection to accomodate jetpack usage by making the ceiling higher and the sniper rifle ledge bigger to make it easier to land on.
While I think they could have been nerfed a bit (should have had a short usage so they were more of a jump pack than a hover), you trade being able to jump up a level by the inability to speed your way to your destination with sprint or protecting yourself with armor lock. You also make a very loud noise as you do so, so you're definitely trading being covert away. Finally, you have a gigantic thing on your back that makes you easier to see and get stuck with.
You could use a grenade jump in a similar way in Halo 2 to go backwards through the seawall on Zanzibar, even though it was intended as a one-way trip for the offense to attack from. The grav lift made it easier to do in 3, but I don't see people claiming the grav lift broke map flow. It IS the map's flow. If you don't want a jetpacker to be able to go up somewhere, you put a damn ceiling or soft kill down. It's not that hard. Bungie's designers weren't fucking helplessly watching as jetpacks rampaged all over their maps, and the idea that they would be helpless to consider the jetpack's impact on the maps is insulting.
Grenade jumping causes damage to the player, as well as wasting a grenade.
Risk/Reward.
Map control and the control of power positions has always been a key part to Halo's multiplayer, and breaking that with a push of a button is not a good thing.
That being said, I think the "Jet Pack" should serve more as a double jump, like you suggested.