So we finally managed to take off after 2 hours on the tarmac, thankfully without hitting the crane.
I got a good look at the crane of the way out, it wasn't directly in front of the runway, but off to the left (at about 10 o'clock). The issue was that it was obstructing the planned "emergency escape path" if we were lose an engine at take-off.
I guess now that they have the performance calcs for an alternative escape route, that the crane will be allowed to stay.