We have done this quite often for editors that have the knowlege to write their own css.  They way we do it, we create a property on the start page of type ContentReference

[Display(Name="Css File Override")]
[UIHint(UIHint.MediaData)] <- off the top of my head public virtual contentreference {get;set;}>

This is how we do it.  Apparently my tablet won't let me edit the property but i forgot to type the property name.  if your using webforms, you can do the same thing but get the property from the start page   UrlResolver.Current.GetUrl(ContentLoader.Instance.Get().Get(SiteDefinition.Current.StartPage).CssFileOverride).  Probably best to do some null checking in there and not put it all in one line but you can see what i am doing there.

Get some inspirations from David: http://www.david-tec.com/2014/02/Using-Virtual-Template-System-for-EPiServer/

Made a really great tool.

Many Thanks

@Valdis: I tried solution It saved Virtuala file in DDS. I can reference my file as href="/assets/css/custom.css" rel="stylesheet"/> as data will be picked from physical file. 

@Joshua: I will try and will update you.

Hi Joshua, 

This is what we also have been doing before. But was not working with my this project. Culrprit was Blob Provider for cloudianry as it was not loading CSS files in Raw Format and on accessing I was always getting NoImageFound.Jpg and in result styles were not applying. I fix that and it is working now.

Regards
/Khurram