Honestly, I think it's fine as is.
And really speaking, I'd hardly call goose scratching his eye a "sub plot". It's a beat, at most. There is however a running gag throughout the movie of Fury injuring his eye and people asking how it is. The bit with Goose was just the punchline.
And for those that think Furly loosing his eye to a cat scratch is anticlimactic, I'm pretty sure if he went into any bar in the galaxy and said "I lost my eye because I pissed off a Flerken", the response is likely to be "You pissed off a Flerken and all you lost was an eye!?"