Qui-Gon nods because, just as Ezra's been asserting, he is right. The partnership between Master and Padawan is a two-way street full of shared responsibility. Yes, as Qui-Gon stated, the teacher is the one who assumes the most responsibility, but that's only a natural turn of events--it's a latent protective paternal instinct present in most Jedi who choose to take on a Padawan. It's the byproduct of the Jedi Order who, despite their insistence in forbidding attachment, turns around and has their Masters take children under their collective wings, forming tiny families in all but blood.

As much as Qui-Gon loved the Order, such hypocrisies didn't escape his notice... nor his ire.

"That is true," Qui-Gon confirms, "and you've done everything in your power to follow your instincts and do what you can to keep him safe. That includes forming alliances you believe to be beneficial."

He gives Ezra's shoulders a reassuring squeeze.

"Whatever the consequence, know that your intentions were good and continue to trust in them and your instincts."