Now, on the topic at hand, I think of Talos as being sort of like nuclear weapons (he can be just as destructive). The empire has given up on its special weapons projects in favor of focusing on conventional warfare, while the Stormcloaks are fully dedicated to their special weapons. If the Stormcloaks win, then man will be in a weaker conventional warfare position, but will have a better chance of harnessing a huge destructive force against the Thalmor.
Seems like the Thalmor come out on top no matter who wins, but in my opinion, mankind and Tamriel would have a better position if the Empire wins. Their rejection of Talos/Shor/Lorkhan is damning, but He is a powerful force even when ignored, and a victory for an empire would allow man to put a less divided front up against the Thalmor in military and political terms.
And thus we have the two positions presented in the first two responses, good start. I guess the issue for me turns on how much of a pause can we expect before a major engagement between the Dominion and the Empire. If we are looking at the long run, with a break measured in centuries I would agree that a dedicated Talosian cult would likely be more beneficial than a united Empire. However, in the short term a Skyrim break from Cyrodil could be disastrous. The Empire is already severely weakened and in chaos, and if another war is only a decade or two away (as I suspect) then Skyrim's manpower and resources are pivotal.
Of course what is missing from this discussion is reliable sources regarding the status of the Thalmor and the composition of their armies. The scenario could play out in dramatically different ways if the army consists predominantly of Altmer or if the regulars are Goblins, Bosmir, and allied Khajit while the Altmer make up a command staff.