I think this is a great suggestion and I would love to see this integrated into Alfred.
Interestingly enough, I found a product this morning called Shortstop that allows you to disable global hotkeys from the menu bar, so if you're working in an application that has keyboard shortcuts that are being over-ridden by your global shortcuts, you can temporarily disable them. It would be much nicer, though, to have this feature integrated into Alfred though as per NeoDarque's suggestion.
In the meantime, I found a hack from Brett Terpstra that I've been enjoying: A useful Caps Lock key, which allows you to change your Caps Lock key into a key macro for Cmd+Shift+Opt+Ctrl and I've since been using it to launch Alfred workflows (it's rare that applications use all those modifiers for a shortcut, so the chance of over-riding a useful function with a global shortcut is lessened).