The solution really depends on what your problem is.
If the problem is that the above ground biome is hostile (i.e. the local animals are hostile), you can:
1. Send sort of reasonably equipped dwarves to kill the animals.
2. Hide underground while the dangerous ones roam the surface, and venture out only when reasonably benign creatures are about (which is my tactic in the caverns).
3. Use war animals (typically dogs) attached to the civilians who are out. Dogs aren't that good fighters, but they can buy you time.
If the problem is that you sometimes encounter dangerous animals:
1. If the animals are location associated (such that aquatic dangers), keep away from these locations.
2. Use 1 above, i.e. send militia to kill them.
3. Use civilian alert burrows to get civilians to safety. Disable outdoors pastures to get the animals to drift inside your fortress towards your meeting area.
Regardless of the above: Make sure you have a secure fortress with at least a couple of draw bridges to close off the entrance, and it is quite useful to have cage traps as well (if they're inside the outermost drawbridge you can close the bridge and then reload the traps in safety), since some animals try to get into your fortess. If you cannot handle/live with animals, you'll probably have significant troubles dealing with enemies.
Some might consider turtling (hiding within the fortess) to be cowardly. I think it makes common sense. Turtling shouldn't be passive either, but rather the time should be spent devicing means to deal with the threats (mechanical defenses, better training/equipment,...). Also, you can turtle in some directions, and work mostly as normal in others (e.g. turtling against a surface threat and one in the second cavern, while working as normal in the first, and preparing the proper break of the third [but you'd probably put this on hold until the other threats have been dealt with]).