Understandably, as both Cyborg and Deathlok were by and large good guys for most of their appearances. But, I guess the answer could be much like the Age of Apocalypse (where some formerly very good X-men were awfully mean) -- some events in the Amalgamverse were so different from regular continuity that a few of the good guys were warped (and some of the bad guys were un-warped, too, I think, though no examples come to mind).
Source: wiktionary