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Perhaps the chlorine is not quite a high enough concentration to harm them, or the Glukkons simply are resistant to it.
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The fact is that chlorine is a very simple substance (it's not even a compound, but an element!), and, as far as I know, would affect many species. The Glukkons would be somewhat affected themselves, even if maybe less severely than Mudokons.
Then again, maybe the thick layer of soot from cigar smoking is what protects their airways and lungs 
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But on your interesting point about it being specific to mudokons, I do think is likely. The game developers might have based it on the fact that stereotypically, toxic gas is green in colour.
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Yeah, probably they thought of a green toxic gas and they realised how funny it would be if the Glukkons died from their own toxic gas so they made it Mudokon-specific...