For the thing with Tobias, that's what makes him so interesting; he's Elfangor's "time-shifted son." Tobias can only exist as the time shifted son, change one parent and he's not really Tobias.
Now it's a matter of the Ellimist's involvement. He's not allowed to interfere with the lives of other species (yeah right) , which means he can't directly anyway, wipe Tobias out of existence. At the same time he can't REALLY undo everything the happened with the time matrix. It still happened, it still had it's affects and he can't just completely negate those events, just like MM3, altering to remove John whatever was permissible, just not by him.
He put things back as they "should" be; Elfangor ran around time and space, did his thing and then when back to the fight, not Elfangor ran around time and space, did his thing, and then went on to do business with Bill Gates
And the Ellimist did have people on his side; the Pemalites where his remember, but since their eradication, no, I doubt he had active units working directly under him. At most it would be only small groups like the Animorphs who he would influence/make himself known to
My god my response are long aren't they?