There are a couple ways to deal with this. First, the version of fear used by wolves and werewolves only affects humans and elves, so if you have non-human units (beasts, plants, etc) they won't be affected. Additionally, the fear caused by wolves and werewolves only affects lvl 1-2 units, so any lvl 3+ units (e.g. Archmages) will not be affected. You can also dispel fear from one unit at a time if you really don't want that particular unit doing their own thing.

What DarrkPhoenix said, plus get some wolfs/werewolves yourself and cast fear first. They are pretty useful early on, but as you start to encounter enemies level 3 and above... Well, you get the point.

I have also just played King's Bounty a brilliant game if you ask me and better than HOMM.
If the wolves cast fear your units don't get taken over but they attack no more units of a level that is above them. One tactic is to use only high level units. Later in the game you can use fear yourself as i have just played a mage and it is the perfect crowd control especially later in the game. I just used units of level 4 and above and all other creatures below could do nothing anymore once fear was on them ^^.

Also, units with a high initiative allow you to discard that sort of problem.

It may let the unit move on the first turn before Fear is used, but you'll still be unable to control them for the next two turns.

Not if this unit neutralizes the wolves or if you use this turn to cast an appropriate spell.

If there's only a single unit of wolves/werewolves that can be quickly neutralized then that's an option, or if it's late game and you can pull out something like level 3 Magic Shackles. However, most of battles where people have trouble with the wolves/werewolves are in the early game where there are 2+ stacks of wolves/werewolves, your own units aren't powerful enough to one-shot the stacks in question, and you don't yet have access to spells powerful enough to completely neutralize the threat.