You forget that Warcraft 3 custom maps weren't free, you actually had to buy the game first. Contrarily, basic DOTA 2 is free. In order to make DOTA 2 custom maps just as free as playing Warcraft 3 custom maps were they would have to charge you 20+ dollars for the privilege.
Now, of course I would prefer it to be completely free, but saying Warcraft 3 custom maps were free is completely untrue, and while I could see Valve doing it (because they are pretty damn awesome and have loads of money) I can't actually see any other game company ever releasing a free engine with free servers that gives them literally 0 money, and won't give them any money in the future.
But yeah, if they try anything remotely like what Blizzard tried to do in Starcraft 2, they are pretty sure to sabotage any hope of the custom maps being anywhere near what Warcraft 3 achieved.
E: Make no mistake Blizzard made tons of money off the Warcraft 3 custom maps, I know I personally bought Warcraft 3 3 times (due to moving and losing the disk), 2 more times then I would have bought it without the custom maps. It certainly made them a ton more money on the game then they would have otherwise, whereas if Valve does this all for free, it will make them no money. It may give them a few more DOTA 2 players (as people who play the custom maps will also play DOTA 2), but unlike Warcraft 3 DOTA 2 is a free game, and it won't really make them any money.