if the guide says he wont ally, then he wont. i did the same thing on my account and i figured it was a bug. your going to have to destroy the brotherhood to progress. it svcks, and is a [censored] design decision from a company built around [censored] games (SWTOR2, etc) but there isn't much you can do about it beyond reload. sorry guy.
It's a perfectly reasonable consequence of your actions. It's not the developers' fault you misread the situation badly. What with the whole "Hardin hates the NCR and wants to retake Helios One" and "Hardin's first quest after becoming elder is to have you murder people with the temerity to sell energy weapons" things making everything pretty damn blatant if you actually *think* about what decisions you're making.
I have little sympathy for people who complain about this. Mind, Hardin would probably side with Caesar if asked.
Assassinate Hardin and stop the trail?
Probably. You'll have to act fast though since you only have a few days, and you'll have to make sure nobody sees you murder him. Mister Sandman would be good for this, if he sleeps. (I think he does?)
Use any cheat to end the quest with the alliance?
Da, if you're on the PC. You need to get the quest ID for "Still in the Dark" - Check the Vault wiki. Then you need to type in sqs
to get the quest stages. Then you can go setstage X where X is equal to whatever stage you're looking for.
If you're on the console, I guess you better hope that killing Hardin keeps MacNamarra in power.
Revert a quick save from before the overwrite? >_>
Unpossible due to how computers work. Once a file is overwritten with another file, the previous one ceases to exist.