The Republicans would have been further ahead to let them filibuster and then use the 'obstructionist Democrats' ploy that worked so well with the removal of Daschle.
I don't think they wanted to use the 'nuclear option', because it would be seen as a power-grab. They took enough of a beating over the Schiavo intervention. The only way for them to prevent filibustering is to work on taking the supermajority of seats in the senate.