I swear, sometimes I feel like I'm the only player who isn't constantly killing their follower(s).

I do friendly fire mine on occasion, but I've gotten it down to a near minimum--even though he's often charging in ahead of me. My character is a mage/spellsword and my follower (Erik the Slayer) is a tank...it's a combination that works really, really well for me, but it might not for you. You may want to try a ranged follower, or even another mage, if you find your tank follower is getting in the way too much. I hear Marcurio's supposed to be pretty awesome.
If you do stick with a tank follower, trust me when I say...learn to aim, and when to hold your fire. The way I play, I usually get off the first (spell) shot as a sneak attack. (Yes, it is possible to sneak with followers.

You just have to find one that's good at sneaking.) Then Erik charges in ahead and takes all the enemy aggro while I sneak around to the side and flank with spells or sword. This means: Erik and I aren't constantly fighting for elbow room--which means I'm far less likely to hit him, and I've usually got a clear line of sight on him and whatever enemy we're fighting. If I have a clear shot, I'll take it. If I think there's even a chance I might hit Erik, I hold my fire or try to move around for a clearer shot.
When it comes to AoE stuff, that's a little trickier. I don't use chain lightning usually, since that's meant for taking down groups, and I'm more of a "pick the enemy off one by one" type. I'll usually use AoE spells as a first salvo though, to do a lot of damage before Erik goes ahead and charges in. I've also gotten to the point where I've enchanted most of Erik's gear with resist magic/fire/shock enchantments, and his health is so absurdly high (he's got ~450 health at level 34 IIRC), that I feel comfortable dropping a fireball or two even when he's in a fight. He'll yell at me for it, but it doesn't do too much damage to him. Though if he's getting low on health I won't do that for obvious reasons. (With Erik, I've had him following me for long enough that I know he has specific lines of dialogue he'll say when his health is starting to get low, and I know what they are. When I hear one of those lines I know it's time to avoid AoE/Shouting, or to break out the Healing Hands spell if I really need him in the fight.)
Shouts are another kind of tough one, but it comes down to aiming again. I'll only Shout when I know Erik's out of the line of fire...either when he hasn't charged in just yet, or is off-camera somewhere. Although this can lead to some Yakkety Sax style antics where I have to run around a room until I know he's out of the (admittedly quite wide) blast radius.
Basically, it's completely possible to use a tank follower if you're a mage. Just keep an eye on them, know when to use AoE and when not to, aim your spells properly, etc. It's not totally foolproof...sometimes Erik will charge on in when I'm not expecting him to, zig when I expected him to zag, whatever. Then I may hit him and get yelled at over it.

Or accidentally FUS RO DAH him into a wall or something. Doesn't happen too often, though.