I was playing earlier about to storm a fort and Hadvar says "Talos be with you" or something like that. So do they still worship him secretly, or was it a joke or something? Or are they just being controlled by the Thalmor, and supposedly waiting to overthrow them.

The average Imperial hates the Thalmor just as much as the average Nord, and no human is happy about the ban on Talos worship.

I suppose it is like any other thing that is forced on you by an invader or opressor.
You pay lip service, but dont really follow through unless there is a chance it will cause trouble.
The ban on Talos is still recent so a lot of people will have grown up worshiping him.

Still, in the end the Thalmor's strategy is valid. All it needs is time for Talos to first become fringe and then more or less forgotten.
History is full of examples where the opressor (almost) succeeded, a recent example being how the English outlawed the speaking of Irish and put all sorts of social and economic barriers in place for those that did. This has since been averted because a more enlightened age with freedom and such was begun and I believe the language is doing quite well now.
But history is full of examples where (parts of) cultures were completely destroyed over time.

Basically this. They're just not allowed to worship him openly.

In Oblivion Talos is all over the place right in the heart of the Empire.

In fact the upscale district of the Imperial City is the Talos Plaza District.

So it does not appear that the Empire or Imperials in general have anything against Talos, and some make actually be devoted to Talos.

This appears to be be simply an undesired result of losing the war to the Aldmeri Dominion. The Empire was beaten hand had to accept the terms of the treaty.

Just because they can't worship Talos openly doesn't mean that they don't do it or believe in it...

When Hadvar said "Talos be with you" basically the empire still worships Talos and that they CAN'T openly practice it because the Thalmor have a "to kill on site Talos Worshipers"

Hadvar says that banishing Talos worship was not the Empire's best move. I believe alot of Empire-sympathsisers also feel this way. The banishing of Talos worship wasn't to annoying anyone, they did not do it out of spite or becouse THEY did not think him worthy. The Thalmor did. The Empire is NOT the Thalmor.

I suppose it's like Shintoism in post-WW2 Japan. Official promotion of the religion is banned, but the victor does not really care about individuals as long as they keep it quiet.

This is how I feel and with all the "looking the other way" about Talos worship by the Empire, I think it's pretty clear how they feel. It was a mistake to concede the banning of Talos to the Aldmeri Dominion but they felt they had no choice if the Empire was to exist to fight another day.

Indeed! The Empire can live without open promotion of Talos, but the Empire's populace cannot live without the Empire. The choice was "No Talos?" or "No Empire?" - which would you have picked?

On another note, it can lead to some seriously great RP and immersion if you RP a Imperialist (ie opposed to the Stormcloaks) but hate the Thalmor and the Concordant (Sorry forgot the full title of that treaty)

Yes, it does lead me to great RPing thank you

The thalmor may not yet have the means to enforce the ban completely, but make no mistake - they are not kinda-sorta allowing talos worship. They capture and torture anyone they catch.

The one thing that the Imperialists and Storm-cloak enthusiasts can agree on - banning Talos worship is wrong!

Seeing as Hadvar is a Nord, he's not the best person to use for a proper 'Imperial' view of Talos.

Now General Tullius....there's a fine specimen of an Imperial man!