it doesn't feel like anything will make it a nice experience like you would expect from an apps keyboard shortcut search.
thought about some fun ideas though
Reading the keyboard state directly from the script filter itself. when you hit F you could potentially detect wether cmd or ctrl is pressed. but it looks like you will not be able to actually enter text in the search field for those cases and you couldn't deal with the arrow,page up,etc keys
or find a way to have a live script filter that auto updates based on whatever keys are pressed independent of what is entered in the search field by by calling an external trigger at the end of each script filter execution. (sounds like it could cause a lot of problems though)
for future alfred updates, it might be something to think about, where you poll a script and give it control over the search field and allow it to do it's thing independently. give it the ability to add icons to the search field for special keys like arrows.