The law states you can receive any damages and also the court can order your landlord to make the repairs.

But because he has likely been unofficially living there all along, I don't see how I can ask him to leave without creating problems with my tenant and risking damage to my property.Any suggestions for handling this situation?  

In VA you are entitled to sue tenants for up to $5,000 of lost costs (I cant recall if its in rent/damages or just in general to cover costs).

I am not sure how you would do this, it is probably also a legal issue and for an LLC since you may not want to damage your corporate protection for a 2 week vacation.   

You will return to her her security deposit if she returns the unit clean and without damages by the end of October.

Also, how would an out-of-state owners usually deal with damages to the property caused by tenants or natural disasters?

There are also some damaged doors that have to be replaced which is a minor expense considering that hollow core slab doors are only around $35 each and I prep them myself for install.

All  damages are deducted from the  security deposit. 

Attempting to interfere with that would place your licensure in jeopardy and could damage your reputation as a professional.Protect your livelihood - let people make their own mistakes and stay out of it.

So I had lunch today with a local real estate investor and he told me he felt discouraged that property management companies he had interviewed were so focused on occupancy and not focused on pro-active preventive maintenance.Example:  a damaged door, waiting for the thing to break so it can be a "billable event" instead of squaring up the frame, tightening a hinge, lubricating the doornob, whatever.