Generally speaking, if the initial delay was due to "extraordinary circumstances" then what follows doesn't matter, but it's not clear from your message whether there were ATC delays in Paris or this is what they consider not flying over Pakistan?
The initial delay at departure (as per FR24) was 2h36, arrival was actually only 2h53 late (although until doors open I suppose could have been just over 3h late), not sure if they agree on the length of the delay?

Especially given that they have stopped flying over Pakistan few days before I would indeed find it unlikely to hold in court that it was really "extraordinary circumstances" if the initial delay revolve around the longer flight path leading to crew timeout.