Failing out of the pipeline does not remove your rank...you can only have rank removed by Captain's Mast. So, study hard, keep your nose clean, and you have nothing to worry about.
You recruiter can enter your recently completed college credits. However, at this point, I'm assuming you've signed a contract. Therefore, it is what it is. If it does not guarantee you E-3, then you weren't guaranteed anything, plain and simple. Your remaining credits can really be entered in your service record at any time.
Used to be (late 80s), you put on E-3 at the completion of boot camp and E-4 after completion of "A" school. I'm assuming its still that way, but perhaps someone who recently went through can confirm that. If you wash out of boot camp, none of this matters, because you won't be in the Navy any more. Wash out of the nuke pipeline and you'll still be whatever rank you were, as long as you haven't had any disciplinary action taken against you.
Good Luck.