If they pull that much current, you WILL blow the fuse in the hub so yes, you need to go with power injection if you want all 100 Pixles on the same controller. Cutting the 12V line is up to you but there are a few things to consider in making that choice.
The first is are you using the same supply for both the feed and further injection. Computer supplies are tightly regulated and if you are using two different supplies, they may fight with each other causing excessive current draw , overheated power supplies, and blown fuses.
The second issue is if one of the supplies or connections to the supplies fails, then the entire load falls on the other supply, once again causing either a blown fuse or a possible overheated CAT5 cable and possible fire.