This is my core beef with so much of MOBA design. Ganking is forcing someone to choose between doing nothing by tower hugging (or just running), and doing nothing by being dead.
Well I like to think that complex, multifaceted decisions are still being made during these situations, they're just being made by teams instead of individual players.
In DotA, when a team of player goes to gank somebody, that gank has to be successful (hopefully with a tower), otherwise it's a huge waste of time and resources that could have been spent farming. A big part of the Asian strategy in DotA is the idea that farming a lane is much easier and safer than going for a risky gank. If your last-hitting skills are good enough, your team will actually make more money farming 3 lanes than ganking one.
So while you as a player may only have a few choice durings an imminent gank, your team, and their team, have already made a very important choice from a plethora of options.
In DotA, during an imminent gank, you have several options:
1. Try to defend the tower alone, and hope it will save you. If there are too many opponents, this probably won't work.
2. Call for help. If you have a competent team, they will be carrying teleport scrolls, and will come to assist you.
3. Hide in the forest. This kind of puts you into a corner, but it wastes precious time for the enemy trying to find you/get vision of you, during which it creates extra time for your team to come assist you.
4. Juke your opponents. If you know the map layout well you can pull off some epic juke maneuvers and possibly get out of the situation alive, and back to your base. Using fog of war correctly in DotA is a quite a pro skill to have. You don't need it to play the game, but it will certainly make you a better player.
5. Teleport out. If you know you're about to be ganked, and you know your allies aren't coming, you have the option in DotA to teleport back to base quickly. In LoL this takes 8 seconds so you'll never make it, but in DotA it only takes 3, and they have to STUN you to cancel it, not just damage you. This gives you the option to hide somewhere safe for a few seconds and escape. You'll still lose the tower, but it's better than losing your own life AND the tower.
In other words, I don't think "ganking" only gives the player 2 options. In League I can see how it does because most of the options I listed above aren't available, but in DotA, your team has many choices on how to help you, and their team has many choices to make in terms of whether the gank is a worthwhile endeavor.
Zoning is forcing someone to choose between doing nothing by running away to avoid the zoner, or doing nothing by taking extreme damage/dying.
Zoning doesn't really exist in DotA, at least not to the same extreme degree as in LoL. For one thing, creep pulling can keep your opponent from zoning you, because the more they keep the lane by their tower, the easier it becomes for you to pull.
Secondly, the denying mechanic makes zoning a bit superfluous and unnecessary. You could miss your own last hits and put yourself in a vulnerable position to push your opponent out of the lane, or you could just deny all their creep instead and accomplish basically the same thing. The nice thing about the denying mechanic is that the disadvantaged player is still DOING SOMETHING. They may not be getting as many last hits as their opponent(s), but they can still get last hits, or attempt to, instead of hugging the tower.
The other side of mechanics I hate is the "I'm doing this to deliberately take away power from you, over trying to gain more power for myself". Most of the stuff in "I'm making you do nothing" falls into this.
I'm not sure what you're referring to here, possibly mana burn? Mana burn is a powerful (and rare) mechanic in DotA, but there are ways to counter or prevent it. For example, Anti-Mage is a hero in the game who centers around the mana burn mechanic (hence his name), but he is far from overpowered or uncounterable. I would go so far as to say he's far from the most annoying hero to play against either. BKB stops mana burn if I recall correctly, so that's one option. Another option is soul-ring which drains health to give you mana, so even being at 0 mana, you can still cast a spell if used correctly. Arcane things on your feet give your whole team a 150 mana boost, so there's another counter to having no mana. A fully charged magic stick gives you 225 mana, so there's another possibility.
Probably the best way to counter mana burn is to just shut down or disable the person burning. The vast majority of mana burn mechanics in the game rely on physical attacks, so if you can slow, stun, or otherwise disable the attacker, they can't burn your mana. Heaven's Halberd is an item specifically made to "disarm" an opponent, so that's one powerful and relatively inexpensive option you have as well.
So I agree with you in one sense: If you do nothing to plan for these kinds of events and mechanics, they basically cause you to "do nothing". But there are many things you can do in advance (starting with the picking screen) to ensure that doesn't happen. This is a very different design philosophy than most games have nowadays (punishing you for mistakes you may have made 20 or 30 minutes ago I mean), but personally I like it. Punishing a player (or team) for not planning better is a good mechanic, even if a lot of people hate it.