It depends on who the republican candidate is. If it's a RINO like Romney, many disaffected conservatives might go the Ron Paul route as their own protest vote.
You said that if Romney is the nominee, many disaffected conservatives might go the Ron Paul route as their own protest vote. Well, those folks would stay home and not vote for Romney anyhow, so what difference would it make? There are a lot of FReepers here who say they will not vote for Romney.
In your scenario, it would be better to vote for Romney as a protest vote against Obama. Obama is the one we are trying to defeat here.