When you read through the reasons, it's perfectly reasonable to refuse. The quay and side roads in around it in the docks are a fucking mess with the parking, and danger issues flagged are fair. It's very unclear down there who's land you're on and where can and can't throw the car. The place isn't set up to cope with crowds being drawn by the market.
Solution here is probably to cut off any customer access to the market from the quay at least, and everyone has to come in from Centre Park Road. Parking needs to be minimal - if you're going there, you're walking or cycling.
The Goulding's site comment could be one that does kill it though. That one blows any plans for that part of the Docklands out of the water for years if a solution isn't found.
The City Council should have been well on top of this before any application went in. They've seen success of the place, and the benifit it has for their plans for the Docklands. At the very least, they'd want to be proactive about assisting with alternative premise if it does go to the wall - a lot of businesses and jobs at risk overt this.
It's similar to the farce up river at Alberts Quay, with new office developments faced in by massive stacks of logs. No firm transition plan in place for the docks while they're both developing and operating as docks.