Given the staggering adaptability of bacteria, and the tendency of gut bacteria to swap useful genes between species like gorram Pokemon cards, I doubt the Vilani diet would have been all that much of a problem. Indeed, I’d expect that after a sizeable number of generation Vilani would have less trouble digesting native foodstuffs BECAUSE their gut flora had adapted to metabolize the stuff.

A LOT of the biology  in Traveller is wrong. The susceptibility of the Vilani to terrestrial diseases is surprisingly not. (and the death toll would have been vastly lower, save for the fact that it happened during a series of wars.)