If Skyrim falls, the Empire's back is completely broken. Thalmor will take power - Black Marsh will eventually come on their radar. If Skyrim is independant, it might be possible for the Argonians to negotiate an alliance with the nords to face down the Thalmor... or Ulfrik might just sign up Skyrim as a client state of the Aldmeri dominion; it'd be a big gamble.
If the Empire takes Skyrim, the empire can consolidate it's strength and try stand up to the Thalmor. It's a long shot but in the long run if the empire suceeds it's ienvitable they will conquer and re-annex black marsh so all you've done is swapped one potential tyranny for another.
But you might also ask yourself "Is the Aldmeri dominion a bad thing?" - the Khajiit have flourished under dominion rule, and the Argonians, like the khajiit suffered awful oppression under the Empire. For them, staying out of the conflict - entirely is the best way to support the Dominion (As long as the empire and nords are killing each other, that weakens both states further), perhaps black marsh would be better off forming an alliance with the dominion, instead of supporting nord independance Vs imperial ambition
Spoiler
They're fighting to free Skyrim from the oppressive Imperials, just as your kind fought against the Dunmer in Morrowind (and I'm sure the force there spared no women or children). You could always just side with the Stormcloaks until the war is won, then kill Ulfric.
Difference is, the argonians didn't deliver blackmarsh/morrowind into the hands of the Aldmeri dominion by doing so, whereas the Nords are going to wrap up cyrodiil AND skyrim in a nice pretty parcel complete with a ribbon, gift-wrap and a "to Thalmor" tag on the top. "Fighting in the name of freedom and liberty" is all well and good when all things are well and right in the world. But tamriel is a complex situation.
Think of the austerity measures in Europe right now - some countries have to cut public spending, raise taxes and inflict a degree of poverty just in other to re-establish their economic standing. If a new party came forward and said "We'll raise spending, and lower taxes", people might support the idea, but they're ignoring the fact debt is continuing to rise and the rules imposed upon them served a greater good. The nords don't WANT the empire's intervention or to live with their rule, when a leader says "skyrim for the nords, and worship talos!" everyone says "yay" because it's what they want - but they're ignoring the bigger problem; the aldmeri dominion - and being imposed upon by the empire might be the only thing that can save them