Hmmm, this isn't a bad idea. I get around this by making sure my locomotives are always in the same spot - so I have a 1-4 (LCCCC) train, and a 1-8-1 (LCCCCCCCCL) train, and if needed I can do a 1-8-1-8-1 train. Then the global fuel station just has the fuel inserted into those specific spots, so it never gets inserted into a cargo wagon.
You could, in theory, also filter what can be inserted into cargo wagons by middle-mouse clicking the slot in the cargo wagon, so that fuel can't be inserted into the wagon. Then if you have 2-8 (LLCCCCCCCC) and 1-4 (LCCCC) trains, the cargo wagon on the 1-4 trains would have it's slots filtered to only accept whatever that train is suppose to pick up, so that it can't get fuel inserted into it. This only works if each train only picks up one type of good though, since the slots can only be filtered to one thing.
I don't have time to work on this right now - if you want you can make the changes (and upload them), I don't have any restrictions on what people can do with my mods.