I missed the destruction sphere in Besaid too... what I did was, saved on the save sphere before Besaid, got Yuna to Overdrive (or Yojimbo) before saving and then walked up to Besaid facing dark Valefor and retried one-shotting him with Zanmato in one turn. Eventually I did it, so yeah. Otherwise he would've just killed my entire party in basically two turns...
I considered doing that, too!
I wanna get all my characters to complete the sphere grid anyway, though, so I know I'm in this for a long haul, hence I'm not in too big a rush.
I could probably take Dark Valefor with my current party, actually. Wakka and Auron both have their celestial weapons all maxed out, and Wakka became a staple in my party due to his ability to hit nearly every enemy and do significant damage throughout the game. As a result, he earned a lot more AP and got more sphere levels than most of the other party members, and has the highest stats in my party n.n;;
I noticed something a little amusing with my Yojimbo, though. Short story time!
At one point, in Omega Ruins, I ran into an enemy that I didn't need to capture, didn't drop significant gil, and I didn't want/need to steal or bribe from it. So, I summoned Yojimbo to make quick work of it BUT IT GOT THE BETTER OF YOJIMBO! So, my aeon got KO'd and I had to take care of the fiend with Bahumut instead.
After that, every single time I face that type of fiend and summon Yojimbo, I do not have to pay him. He will immediately launch 1-2 attacks without any request for payment from me. I'm unsure if this is a penance, for breaking his "contract" with Yuna to be amazing as an aeon, of if it's some personal reaction, like "You bested me once, never again! This battle is personal and I shall not fall," in which case he kinda forgets/forgoes the fact that he's a mercenary.
This doesn't happen too often (Maybe 4 times now) because I try to avoid relying on summons (only Yuna gets AP) as I'm farming for AP/sphere levels. But it definitely happened, and I definitely noticed!