The Tavern

Actually giant flinging rocks. As a spell caster in mid game.

having a medium shield and/or repelMissiles really helps. With ideal tactics you can take them down as long as they don't 1-shot you because they're slow and attack you at the edge of LOS. Also they run out of rocks, which makes them easier if the fight goes on for a long time.Keep your escape options open.
Many spell casters will have enough burst damage to take them out quickly.
Also I don't know what you consider the mid-game, but earlyish on you can avoid them.

A spellcaster still can have defenses. Train fighting and dodging a lot.

Spells can take them out from a distance, which is much easier than with melee, since giants hit quite strong, but they do not move faster than you, therefore you can keep a safe distance. My usual spellcaster characters can kill stone giants earlier than most of my melee characters.

Giants or cyclopes? Cyclopes are slow, so you can walk away from them.

Stone giants aren't slow (or, if they are, it isn't shown on x-v). Besides better defenses, your best bet would be to learn some long-range spell like orb of destruction. Or try to lure and isolate them and use summons (from scrolls or evocables or gods or spells).

*also* if you don't want to get pelted with (ranged attacks generally, but large rocks in this case), have a meat-shield in the way, a good choice is a nonthreatening monster. Even something that not nonthreatening, but won't-do-as-much-damage-as-a-giant-throwing-rocks might be a decent choice, particularly if they don't move faster than you and you can string them along back to a staircase (Which would let you escape from the rock-flinger and kill the meat shield at your leisure).

Walls are also good, but they don't follow you when you retreat.

Allies are are also ok, but they die, which is nice when they're an enslaved thing, but they also tend to walk *towards* the thing you want to block which sometimes makes it harder/more annoying to keep them in between you and the rock-thrower. (They're less meat-shield and more "helpful distraction")

Note that this isn't a very good tactic against frost/fire giants who have penetrating attacks, but for cyclops and stone giants it works pretty well (Also helpful for early centaurs, as you generally want to get them into melee range, so if you can wait for a turn or two with a rat in the way, you can get them to walk right up to you without pelting you with arrows).

Also if there's *really* no way to prevent several rounds of ranged rock-fire and there's any reasonable chance of it killing you, read ?teleport, and do it sooner rather than as a last ditch effort.

Re: meat-shields, allies can be good blockers in this case since cyclops and giants tend to have not much ammo and will waste it hitting your buddy, allowing you to deplete their stock. (The projectile can still miss the ally, fly past, and hit you.) If you block line of fire with a hostile the giant just won't throw.

Fulminant prisms can be placed where you want in a single action and have no ev.

Spires have low ev but but of course you cannot place them precisely in the newest versions.

Like others in this thread I suspect you've trained too low defenses, but it's hard to tell with this amount of information.

Thank you guys! I will implement the suggestions.