Read The Infernal Devices.
Brother Zachariah only became a Silent Brother because of a Demon-inflicted addiction to Yin Fen. If he hadn't become a Silent Brother he would have died,which would have destroyed Will Herondale and Tessa Grey.
In City of Heavenly Fire, Brother Zachariah tries to heal Jace. However, when he touches him, the Heavenly Fire is absorbed. This burns away the Yin Fen, thus meaning that the runes that needed to save him are reversed, turning him back to a regular Shadowhunter.
It is also stated that Zachariah is more human than most of the Silent Brothers, as he wasn't able to take all of the runes. That is why he looks different. He is also just as powerful as the other brothers, as he and Tessa resided over the protection ritual for Clary.
Silent Brothers are also more angelic than regular Shadowhunters. This is because they have sacrificed some of their humanity for more Angelic power. This allows them to bear marks that would normally be locked for other Shadowhunters. There is nothing evil about the Silent Brothers, they have just chosen a different path to the rest of the Nephilim.
"In exchange for their special abilities, they have given up some of their humanity, moving farther from the Earth and closer to Heaven than the rest of us." - The Shadowhunters Codex
Normal Shadowhunters can only bear the angel's runes that are found in the Grey Book. However, the only 'evil' runes that we ever see, are those worn by the Endarkened, and the Rune that binds Sebastian and Jace.