I do not believe Ron Paul can fatally damage the GOP. I do believe that many hardcare Ron Paul supporters wish he could.
You are confusing the anti-war support for Ron Paul now with the anti-war issue of the 60’s. The young supporters of Ron Paul are not worried about having to fight a war as the college students of the 60’s were. There is no draft now. They are attracted to Ron Paul with his message of freedom, smaller government, less taxes, getting out of SS (most of them do not think it will be there for them), etc.
Plus, the economic situation of most young people is very bad. Wages have not gone up enough to compensate for the increase in inflation. Many college students have to take out large amounts of loans to get through college and they know that jobs, which would allow them to pay off the loans fairly easily, are not out there now.
The anti-war message might have drawn them to Ron Paul, but the ardent support is based more on his conservative, small government principles.