How about declaring interfaces?

interfaces.d.ts

interface IMainHelper {
    //... 
}

main_helper.ts

class MainHelper implements IMainHelper {
    //... 
}

other_file.ts

/// <reference path="./interfaces.d.ts" />

import Injector from "./injector";

let mainHelper: IMainHelper = Injector.injectMainHelper();

Note: If you add the reference to your tsconfig.json you won't need to add it in the file.

Update

I just tried and if you have two files:

test1.ts

class MainHelper {

}

var Injector = {
    injectMainHelper: function() {
        return new MainHelper();
    }
}

export default Injector;

test2.ts

import Injector from "./test1";

let mainHelper = Injector.injectMainHelper(); // mainHelper is MainHelper

TypeScript is able to infer the type of mainHelper. If you don't add the type the compiler will automatically detect its type.

If you have something more generic like:

var Injector = {
    injectSomething: function(somethingID) {
        // find something and dependencies
        return new Something(..dependencies);
    }
}

The solution would be to use generics:

let mainHelper = Injector.injectSomething<MainHelper>("mainHelperID");

But in that case you will need interfaces once more...