A few things strike me here.
It seems you're emphasizing the word "civil" when the only thing that matters is you have a permanent protection order filed against you. I'd be interested in knowing what state you're in as procedures do vary a bit.
In my state a temporary order would have been granted first. This would have been done during an ex parte hearing. This would have been the first opportunity for someone to decide an order was not appropriate and deny the petition. You would then have had an opportunity to defend yourself in court--with a lawyer--against the petition. This means you had a chance to tell your side of the story to the judge. The judge found her more credible, you lost, and a 5-year order was granted and entered into NCIC.
Now, your state likely has its own version of Lautenberg restrictions on gun possession. Those can come into play, but what really impacts you are the federal restrictions. Put simply, you are prohibited from possessing firearms and the government is prohibited from furnishing them to you until the order is expired or otherwise nullified. I have never been involved in a case where a permanent order, such as was entered against you, was nullified prior to expiring but that doesn't mean it can't happen.
The specific prohibitions that apply to you are found within 18 USC 922 (a)(8)(d)(8), 18 USC 922 (a)(8)(g)(8), 18 USC 922 (a)(8)(h)(1) and (2).
That covers enlistment in my view, because you can't possess anything that goes bang in any way.
As to any potential clearance, if I were investigating I'd be very interested in any potential poor judgment, and I would definitely be talking in depth to the woman who filed the order. These are things you should be prepared for if you choose to pursue any cleared job outside the military.
It's probably not what you want to hear, but it is what it is.
