I'm the only one who discussed two years ago about the implication of Restraining Order (Order of Protection) in context with Naturalization application. You might try to find some of my old postings on this issue to know the full info. But in short, you have nothing to worry about it because it won't hurt your naturalization application even if USCIS would come to know about it.
In some states, like NJ, it's mandatory for courts to take the fingerprint of the person whenever a restraining order is issued against him/her. But those fingerprints are not forwarded to FBI or any other law enforcement agency; rather they are kept on state level. Thereby, restraining orders never show up on FBI report.
Don't even dare to tell the officer about Restraining Order unless you are specifically asked for. And make sure to take the copy of Restraining Order complaint and the Order at the time of interview.
Just because there is a restraining order against you, then that doesn't mean that you have committed a crime. That means, no crime here whatsoever. Restraining Order proceedings are civil in nature even if a restraining order is obtained in a criminal court. I know that it was family court that issued the restraining order in your case, but if parties are/were not related, the matter for restraining order is heard in a criminal court.
And since your pending N-400 has nothing to do with 3 yrs rule in context to naturalization laws, then it doesn't matter if you guys get divorced. But if would have filed N-400 based upon 3 yrs rule of being married to a US citizen, then your N-400 would have denied without a doubt. But not in your situation because your case is based upon 5 yrs rule (I assume).
There is something you should know. If you would ever violate the restraining order before becoming a US citizen, then you will be deported for lifetime under section 237 of INA. Nobody would be able to save you then, even if you get remarried with another US citizen or would have children born here. There is zero tolerance policy on violating the restraining order. So be careful. It could be possible that your wife might try to trap you in violating it so that she could make you deported as I've seen this happening hundred of times. That's why it's very important for you not to get trapped even if she would try to be goody-goody because you will end up being deported then. Nobody would be able to protect you from deportation. Read my lips-Nobody.
Good luck.