The abillity isn't very clear as who is effected.

A Greatswordsmen is fighting Skellies to the front.

If I side charge the already engaged unit and it must attack me, will the Battle of Wills effect the entire enemy unit so that the skellies enjoy its protection?

Yes, it's the only reasonable answer. Result 6+ spells out that the whole unit is affected, otherwise GW use the term 'the enemy' on the other results.

However, in a multi-combat enemy characters with higher I would be able to strike before Battle of Wills kick in, if they can attack another unit.