Sure, but it was Mede who made the anti-Talos ban official and started putting out propaganda against Talos worship. As Ondolemar says, the WCG made Talos worshippers not only heretics but traitors, and made support of the Thalmor part of the imperials' duty.
Normally when you have a cease fire, neither side is happy and both have to give up something. What exactly did the Thalmor give up? The WCG was a terrible move. Not only did the imperials give up their strongest weapon (Talos) and alienate their strongest support base (Skyrim), they also handed the Blades over and unwittingly contributed to Alduin nearly destroying the world.
I think you're playing a bit too much into this Imperial anti-Talos thing. The Imperials aren't arresting people for worshiping Talos. In fact, it seems they're making an effort to look the other way. It is the Thalmor that arrest Talos worshipers and deem them heretics. Considering Cyrodiil, unlike Skyrim, borders two Dominion provinces, it's hard to blame the Imperials for not being as openly hostile towards the Thalmor as the Nords.
Yes in hindsight the Concordat was a bad move. But as I've said before, hindsight is 20/20. As I said before, a lot of the Empire supported it simply because it would end the wear. And as I've said before, when the hostilities between the Empire and Dominion are reopened in the near future, the Concordat will be invalidated and the mannish nations will get a final chance to redefine who they can and cannot worship. And I feel that with with a three province Empire than a two province Empire and a Stormcloak Skyrim that hates them.
Sure they're using them- see, Thorald Grey-Mane. Whether they hate them or not, their actions don't show it.
They're not using them. They're merely aware of the fact of the Thalmor arresting a Stormcloak supporter.
Edit: I don't think either of us will be convinced of the other side. Neither side wants to change their mind and decide that they chose "incorrectly". Personally, I'd like to see DLC that continues the story and in the end ensures that either side can work out.