I got a letter in the mail two days ago informing me Sallie Mae is the new servicer of my Direct Federal Student loans.
I left undergrad with $24k in Federal loans and $13k in a Minnesota SELF loan (through MN Dept of Higher Education).
This is where I stand now, according to Sallie Mae on the $24k Federal student loan.
There is no way to "get in trouble" by making extra payments on your loans. Sallie Mae doesn't care if/when you pay early, they only get involved if you miss a payment. While you're still deferred, feel free to apply your payments however you think is best.
Where did you see this information about a "back-end" or "repayment" fee? Sallie Mae services both federal and private loans, so if you were just poking around their website, maybe you were looking at terms for a different type of loan? If you have questions, I would read carefully over the terms for your loan (which should be available through your Sallie Mae account online, or by calling them) and then call them with any questions.
As with all lenders, stay on top of your loan status. Be proactive about updating your contact information, checking that payments have applied properly, and reaching out to your lender if you need a new repayment plan, deferment, or forbearnace to avoid a late payment.