Disclaimer: I don't know anything about YA. I don't write it and I haven't read it since I was a YA myself, so I don't know what level of sympathy and realism is required.
But as a writer, I think you're asking the wrong questions. Characters can be objectionable. Heroes can be flawed. Does the narrative regard their flaws as flaws? That's the real question. I don't like reading historical fiction in which injustice is erased or glossed over. Ideally for me, it should be present as part of the picture, but not completely dominating the narrative (otherwise, injustice becomes the whole point of the story, it gets too preachy, and it would be better as nonfiction)
As someone who's been to Central America, I think they have their own issues with racism and colorism that are quite separate from anti-Americanism. I don't think anti-Americanism is prejudice per se, anyway... it's just acknowledgement of a political reality and desire not to be totally dominated by a vastly more powerful country. The racism is something different. Those countries were dominated for hundreds of years by slaveholding white European elites (just like the United States), so even though they're much more multiracial than the United States, a lot of that attitude is still there in the present day.
Realistically for that time period, unless your character is himself Afro-Honduran, he'd likely be racist against the Afro-Jamaicans, not because they're associated with the US, but because they're black. Maybe that's an issue he works through and gets better on throughout the course of the book. Or maybe he's the rare person who was better than that. I'm sure there were crusaders for racial justice in Honduras too.
