Instead of failing at the merge step, why not add a label saying "OK" for pieces where the state is correct? Then have a system monitor for changes and add/remove the label as appropriate.
Then they won't be able to submit if the label is missing, and you'll have a break glass mechanism of adding the label manually (by a suitably empowered admin) if you need to push something through in emergencies.
Oh and if the remote tracking system falls over or suffers from poor load/design then at least it won't hose your repository and have users blaming that instead :-)
Alex
Sent from my iPhat 6