You could use the filling in this recipe with or without the chocolate chips. Whether it can be frozen I don't know:
KILLER CUPCAKES (makes 20-22)
Cupcakes:
4 squares (4 oz) semisweet chocolate
1 tsp vanilla
2 sticks butter
4 eggs
1 1/2 cups sugar
1 cup flour

Preheat oven to 350°. Line standard muffin tins w/paper cupcake liners. In the top part of a double boiler over simmering water, melt the chocolate w/the vanilla & butter. In a large bowl, beat the eggs until thick & add the sugar. Beat in the flour. Fold in the butter-chocolate mixture. Spoon into the prepared tins, filling the cups 2/3 full.

Filling:
8 oz cream cheese, softened
1/4 cup sugar
1 egg, beaten
Dash of salt
3/4 cup semisweet chocolate chips

Mix the cream cheese, sugar, egg & salt until just blended. Stir in the chocolate chips. Drop a rounded teaspoon of filling onto the top of each cupcake. Bake 30 minutes.~~

There's a White Chocolate Cream Cheese Frosting below. Judging by the recipe, these can be frozen & thawed in the refrigerator. I'd love to hear how yours turn out.

Here is a link that might be useful: Red Velvet Cupcakes

Cream cheese really doesn't freeze well, so I would fill them after they are thawed.
RL`