It's difficult to see someone we care about turn away from the path of wisdom and make choices we're certain will hurt them in the future. It's hard when they've never known the Lord, but in some ways it's even more heartbreaking when they have walked with Him for a ways and decided to reject Him for their eternal future.
The pain of betrayal from Judas was much more powerful than the acts of the Sanhedrin because he had lived with Jesus and His other disciples for three years and the rejection was as personal as possible. This was not a stranger looking for an opportunity to kill Him; this was a beloved friend who turned his back on the One willing to give him everything. When we love someone, it is hard to see them making decisions that will lead them to pain, possibly death. Beyond the obvious consequences of the betrayal, it was surely difficult for Jesus to see Judas make decisions that lead to Jesus' death, his own suicide, and the ending of any possibility of joy for him.