The decision of whether or not to prosecute always falls to the DA/PA. But even returning the money wouldn't necessarily save the OP. Think of it like a shoplifter who gets caught, but returns the goods afterwards; they can still be convicted of shoplifting.
I'm not going to look it up because it doesn't really matter, but I thought I read somewhere that the Postmaster General had the authority to prosecute criminal mail offenses without a local DA/PA. It doesn't matter because OP committed a federal crime and it is possible that she could be prosecuted and convicted, but I really doubt that anyone wants to get into the "what are the odds?" game.
My question is more about whether she had the right to actually deposit the check or not and then transfer the funds, without the consent/knowledge of her husband.
I'm actually hanging on for one or two people in particular to chime in here because there has been a very recent thread touching on a similar premise.
Three issues:
1. Was the check deposit illegal?
It all comes down to the check and what it was for and how it was written. For most checks (such as a paycheck), depositing it into a joint account without signing his name is perfectly acceptable and no charges would be filed (but see below). However, SOME checks involve conditional endorsement where you are affirming some set of facts by endorsing the check. For example, the check might say "by depositing this check, you affirm that you are the person whose name is on the check" or other conditions. If OP is in violation of the conditions, she can be charged with theft.
Conditional endorsements often occur with retirement checks (which is the situation that came up in the other thread). OHRW says that it may be the case with a 'school check' but I'm not as familiar with those, so I don't know how common that would be. In the end, though, it comes down to how the check was written and whether there were conditional endorsements.
2. If OP had actually signed the other person's name, that would be fraud. Being married does not give you the right to sign the other person's name to a document. You can sign their name with the appropriate information (such as "John Jones by Jane Jones", IIRC, but simply signing his name is wrong. However, that doesn't seem to apply here - OP signed "for Deposit Only" which is perfectly OK (as long as the conditional endorsement in #1 doesn't apply.
3. The bigger issue is misappropriation of marital funds. OP took money that was AT BEST marital and possibly solely the other person's money and transferred it into her own personal account. She will certainly be required to account for that money.
a. If the money was his separate money, she will probably have to return it, even if she used it for marital expenses.
b. If the money was marital, she will have to account for it. If it was used for normal living expenses, marital bills, or legal expenses, then it may not be an issue in the end, but she will still need to provide an accounting.