It's also important to note that the idea of unjust but holy sufferance is _central_ to the conception of the Messiah and to the Jewish religion more broadly (the Messiah being the culmination and epitome of the Jewish faith, it makes sense that he will suffer the most). You can track the development of this theme through the old Testament, of course Exodus is classic but it matures quite a lot through Psalms and the books of the prophets before reaching its apex in Job. So it's a crucial part of the Messiah narrative that Jesus suffer, be ignored and vilified by his own people, and finally handed over to the enemy by the Pharisees, those who claim to maintain the law of Moses but actually corrupt it to gain worldly power. If his life is a gallery of suffering, then his disciples should be his solace -- and often they are. But even they let him down, lose faith at critical moments, or fail to understand even when they really want to. That's at least my interpretation of the underlying aspects behind this behaviour in the disciples.
Maybe that's enough to go some way to answering your question, but I'll also say this: naturally we'd like to know whether a gospel passage (pericope) is historically valid (of course this is just a matter of likelihood, not any kind of "truth"). An important tool used by Biblical scholars for this purpose is the criterion of embarrassment -- basically, it observes the same thing as you, OP, that there are plenty of passages in the gospels that don't fit in with the "literally sinless perfect son of God" vibe. The criterion of embarrassment posits that these passages probably survived because they were widely-known facts of Jesus' life, so all the zealous authors could do is sugar-coat the incidents as best they could. The relatively thin layer of sugar in Mark compared to, say, Matthew, or especially John, is another argument for its priority. There are some good examples here [https://en.wikipedia.org/wiki/Marcan_priority#Hard_readings
] if you want to see more, but if you just finished reading Mark they won't be new to you.
There are other criteria of authenticity that scholars use to evaluate gospels, too, of course; in the end, it's a matter of taking _all_ the possible evidence you can find, weighing them against your criteria, and making a judgment call about the likelihood of the historicity of the event. This is a kind of faith -- but not a religious one! Rather it's a social-scientific one, and it's needed when evaluating events from the life of Brutus or Genghis Khan, too. Actually, compared to those figures, it's kind of amazing how much material we have on Jesus considering his insignificance at the time he was alive.
Since this is /lit/ I'll recommend the book that I found most invaluable in learning all of this. "A Marginal Jew: Rethinking the Historical Jesus" by John P. Meier is an incredible piece of historical scholarship, really a pleasure to read. It runs to five volumes, so it's pretty hefty, but the first two alone will equip you with more knowledge than you know what to do with.