Fury does add much needed survivability to Ephraim, as without it, all his defensive stats are somewhat mediocre thanks to his awful speed.
You should think about wether you really need Ephraim to sweep more then one unit. If so, then you would need to pair him up with some form of healing anyway, because the legendary refinement doesn't remove the counter attack from your opponent (and red sword units hit hard)., so you will probably be below 90% without Fury anyway.
In other words, go with Fury.
Well I'm also wondering if taking that upgrade is actually the better option.
Ephraim's role is mainly to be a Buffer with tanking ability. I guess it depend on your gameplay but for me he very rarely initiate on an ennemy but rather tank them during ennemy phase. In that situation his refined weapon would help much.
I guess it also depend which build you are running.
I personnally find is best build to be Triadepte + Lancebreaker.
Triadepte allows him to take very low damage from swords and deal huge damages in return. Lancebreaker allows him to tank and eventually kill lancers.
In my opinion fury isn't as usefull as he will still get doubled by many and triadepte will allow for more tanking, same goes for lancebreaker as he can't get doubled by them.