You know what I find curious? The fact that the Roms side with the Kobali with very little thought. Think about it:
One of the things that defined Hakeev as a evil person were his dealings with the Elachi. Are there not similarities between the Elachi and the Kobali?
There have already been comparisons between the Kobali and the Borg, but there are a few notable differences: namely, that assimilation is reversible (the Cooperative), but transformation is not. In fact, at one point Rom players burn the pods full of half- transformed Elachi rather than freeing them(with the exception of those who have not started the process yet). This implies that the process is irreversible, or else you would have presumably rescued the victims, many of who were probably with you on Virhnat.
I think that a big difference is that the Kobali aren't converting living people, whereas the Elachi are forcibly converting living people. Also, even if you have reservations with the Kobali's methods, the game makes it clear that Gaul's folks are hateful jerks who need to die, repeatedly. After Gaul's deposed, reevaluating the alliance might make sense, but while he's in power? Set phasers to "charbroil."
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I think that a big difference is that the Kobali aren't converting living people, whereas the Elachi are forcibly converting living people. Also, even if you have reservations with the Kobali's methods, the game makes it clear that Gaul's folks are hateful jerks who need to die, repeatedly. After Gaul's deposed, reevaluating the alliance might make sense, but while he's in power? Set phasers to "charbroil."