It should be valid, till war start again with Thalmer who will now be much more likely to win.
More likely does not gaurentee victory. Hammerfell could not be conquered either. Skyrim would theoratically also only have to close down a few mountain passes to keep the enemy out for a very, very long time.
Also, if Cyrodiil would fall there is a chance that Skyrim could ally itself with other countries like High Rock, Hammerfell or even Morrowind to stand together against the dominion, an independant Skyrim would have a harder time defending against the dominion in open battles but would likely be better able to protect her own borders then they would be in the Empire.