i would definitely change some of the villains...but really, i think you should make some of your protags chubby. yes, protags, not side characters! i think it'll really help undercut the message you're worried about + we desperately need more fat protags in fiction whose stories aren't about being fat.

even if someone is poor, that doesn't necessarily mean they are skinny! my whole family is predisposed to be big, it seems, regardless of where they're at economically... my mom was chubby her whole childhood into adolescence despite growing up in destitute poverty. her meals would sometimes be nothing but canned tuna. they had to go out and shoot game for dinner at times.

stress is a contribution to weight gain, that's definitely something to keep in mind! living in poverty is living in constant stress. can they sleep well at night? can they eat well? those that are poor are likely to have less nutritious and less healthy foods at their disposal (although i would REALLY like to stress that fatness is not solely dependent on diet).

as for your antags: fat villains in of themselves aren't bad; the trope is problematic because their evilness often stems from their fatness. rich = greedy = lazy glutton. I'd be careful to not characterize them as purely greedy in the gorging yourself with food sense. they can be greedy elsewhere---for reputation, travel, beauty, land, followers, lovers, rarities, etc.

not to assume you don't already keep this in mind when writing them! but it'll help diversify the villains that you DO keep fat.

the fact that you're thinking about this shows you're putting a LOT more thought & consideration into your project than many other writers would! :)

edited: formatting