I routinely have three or four Screen Sharing sessions open when I'm managing multiple computers, and I'm hooked on my Alfred Workflows.
Toggle Alfred is what we all do as a workaround. A different Alfred Hotkey would pose a problem for machines one uses both directly and remotely.
One could propose to Apple that remote computers get first dibs on processing keystrokes, so to activate the local Alfred one would have to first move focus away from the remote screen. Good luck with that.
Alfred has become a great program because it is open to suggestions.
How would I code this? Presently the Alfred Hotkey toggles Alfred. This is wasteful of precious bandwidth, because Escape also exits Alfred. Instead, Alfred has a valid claim on the Alfred Hotkey when it isn't active. How should Alfred handle a second instance of the Alfred Hotkey, once it has focus? Deactivate and pass the keystroke on.
In other words, if you want to just deactivate Alfred, use the escape key. If you also want to pass the keystroke on, use the Alfred Hotkey.
This is the easiest kind of code change, because there's no interface to change. Perhaps a note in the documention, but the Alfred GUI stays the same.
This is so obvious, I'm surprised it isn't the default for all application hotkeys. I'm stunned that Apple hasn't published a user interface guideline insisting on this behavior.
When a remote Screen Sharing session has focus, the effect would be to send the Alfred Hotkey to the remote machine. This is easily learned; it's human nature to try again when something doesn't work the first time.
Most of the time, one shouldn't even notice this proposed change. The default Alfred Hotkey, or whatever hotkey one settles on instead, is carefully chosen to not already be in use. It should mean nothing to any program other than Alfred. The only circumstance under which one should notice this change is while screen sharing to a remote computer with the same Alfred configuration, in which case a second instance of the Alfred Hotkey would actually work.
I've requested that Alfred consider this change.