Her song in the zoo more or less already showed there was more depth to her and what was going on, which added to her bitterness towards Earth she showed to Peridot.

The trial just conflicted with what we saw and made things more suspicious then anything. You really couldn't genuinely believe that Yellow had malicious intentions with Pink.

An interesting thing to note though is when Blue gets upset and first uses her Depression Wave during the trial. Every other gem gets visibly upset but Yellow just gets a few tears in her eyes. Sort of like a certain Lazuli who managed to shrug off her attack because she, "felt worse."

(Plus it's hard to make her a "cookie-cutter" villain when she's immediately turned into a good guy within 2 seconds.)

Not really a good guy, it's just a ceasefire.