What exactly is each elder dragon's area of magic?
Zhaitan - death (grey)
Mordremoth - earth (green)
Primordus - fire (orange)
Jormag - ice (white)
Kralkatorrik - ? (purple)
"bubbles" - ? (blue)
Are their magics in pairs?
In Omadd's machine they appear in two pairs of three, which confirms the above.
Bubbles, Mordremoth, Primordus
Kralkatorrik, Zhaitan, Jormag
In that sense, destroying Zhaitan and Mordremoth would have taken out two dragons on opposing magics, thereby returning the Alchemy to relative stability.
However that doesn't explain as well why destroying both Primordus and Jormag could cause the destruction of Tyria rather than simply canceling each other out.
Perhaps, because the remaining dragons would absorb all the magic, they would become too potent...
However, I find it interesting that Kralkatorrik is purple, and purple is usually associated with illusory magic. If so, this means the opposite is reality. So if that pair absorbs all the dragon energy... reality and illusion would begin to clash, destroying Tyria in the process.