First of all, it looks like you are mixing up two different notions: console application and command line. You can always use command line, event without console. You can even develop console and windowed application using exact same code processing command line parameters.
You can use conditional compilation, of course, but this is not the best option, and not the best way to organize software in a form good for maintenance.
I would advise to abstract out user interface so your application could use two different front ends as two (or more) different applications; one of them could be a console application, another one a WPF or
application. You need to put them all in one solution. Most of the code should be in the class libraries used by two or more applications.
By the way, you can use my easy-to-use library for processing command line parameters: Enumeration-based Command Line Utility
As to the Revision Control: doing even the simplest work without Revision Control is just silly. I would stop everything and implement proper development procedures with Revision Control system.
See also this discussion: Revision control systems, which to choose from?
Please also see my past answers on this topic:
Needs some words of wisedom to set up and/or use a server
Make an unclickable form
How can i structured to arrange source code when i create a new solution
If you read these answers, you will probably understand my point of view I going to tell you below.
Subversion is not "freeware", not at all. It is Open Source, which is absolutely different thing
. Will somebody tell you that "Open Source is bad"? Even it they won't tell you than, based just on the fact they already told you: the ugly truth is this: you are working with extreme idiots
Therefore, I don't know how to help you. Certain things are not curable. If you want, show them my post. They can easily contact me through CodeProject and discuss this problem, but I doubt they will. :-)