It will be different. Rubio will be nominated and then go on to win the seat. Whereas Specter had the full force of a republican presidential election and the president at his side, Crist only has the support of the senatorial committee for the primary. Without a leader of the party, other members will stray and support Rubio. Crist also gave full-throated support to Obama's stimulus package and embraced Obama. That's a killer in the primary. Once Crist loses the primary, Rubio will immediately get the support of the committee and beat Meek handily.
I agree, Rubio is in a stronger position now than Toomey was in PA 2004. The GOP as a whole is of course much more concerned about ideological purity than it was in '04 when Specter could still be considered a Republican.