So this chick Alea or whatever sent me to kill some wolves but I already took them out so now the marker is just to a blank cavern with nothing in it. Will the wolves eventually respawn or is the companions questline [censored]?

Respawning takes about 30 game days, I think.

Whether or not this specific quest is effected, or they will respawn, I cant say.

The answer is: yes, to both.

Always save right before entering Jorrvaskr because there are quest-killing bugs associated with a few of the Companions' quests.

You might try talking to Aela again. There may be a dialog option along the lines of "I don't want to do that job". I've seen this with the random quests available from Vex and Delvin of the Thieves Guild. I had one that I kept failing at, and in frustration I went to Delvin and opted out. He wasn't too pleased, but he gave me another quest.

You'll have to reload.

This bug hasn't been fixed yet but happens A LOT. Always save before entering Jorvaskr. The location for the target is randomly picked upon talking to a member of the circle.

If you keep on drawing one at a location you've cleared then reload. Because even IF the area has respawned the target Boss enemy never does. You can clear a whole dungeon to find your objective marker hanging above the one guy who never got respawned.