To be fair the leak was fun to mess around with and it was awesome to play a halo game on pc, however it wasn't without it's issues, mainly legal ones. Project Contingency has happy chugged along without any issues since they followed rules and acknowledged that Microsoft had the power to shut the project down, interestingly some of its developers have moved onto their own projects using the skills they obtained. Everything from the engine they used to the in game assets were their own/ another companies and since they were operating as a non-profit program they aren't infringing on Microsoft's policies.
I don't find it a coincident that the DMCA was issued when multiplayer was first shown off/ teased, Microsoft and 343 must of known about Halo Online's modding community from the number of posts here on /r/Halo, /r/xbox and /r/pcmasterrace/. ElDorito were (and still are) using Microsoft's assets and threatened the potential of a western port and its success since why buy a full priced game or deal with MT when you download this free version?. IF they had used the framework of the Halo 3 engine and created their own assets it would be harder for Microsoft and would cause a greater backlash from the PC community if it were to be shut down. Halo Online however was never meant for Western markets especially in it's current state, if it was to release over in America and Europe it wouldn't be surprising to see all micro-transactions gone or having it replaced with a straight up Halo 3 port.
The stupidity of the whole situation is that even if Microsoft hadn't of intervened the population for the ElDorito version wouldn't of gotten higher than a few hundred, a thousand at best, such a small community wouldn't be a issue and would of happily migrated to a Halo 3 port or appropriately designed Halo Online. Even worse is that for multiplayer to work they had to bypass the login system, meaning that players could easily create new accounts for cheating and since most of the game ran on the client side it wouldn't be too long till someone figured out how to remove textures. Furthermore the small population would make it so new players would find it hard to get involved in the community and since it is (and always will be) illegal,streams ,competitions and future hosted files will be shut down. And lets not get started on the biggest issues of most multiplayer pc games, that being poorly done ranking, meaning low level players can get partnered with just about anyone, the best example this are "NOOBS WELCOME" servers on BF4 were most of the players are level 140.
In short, ElDorito should of seen this coming and no one should be surprised, are Microsoft being the bad guy in this situation? No, they're protecting their IP and assets, if they allowed this to happen it could of snowballed into something major. I just want to put here that I am mainly a pc gamer and would love for Halo to release on PC, though I understand Halo's importance to Xbox and Microsoft, hell, I even own a Xbox One JUST for the MCC and future Halo titles.
Should Microsoft release Halo on pc, I see no reason why they should, Halo has remained console exclusive since 2007 (8 years ago) and if they did they would have to release the MCC, this would only cause more issues due to the MCC current state and the coming release of Halo 5. Furthermore if they released ANY main title Halo game on pc the community would demand more and more, reminds me of a Fallout 3NV quote; "Feed a man for free. He'll be back asking for more. Feed a man a bullet. You won't hear from him again" . Alas Microsoft has yet to feed the pc community the bullet (saying that Halo will never come to pc)