Baking a Brie with the outer rind broken
You cannot really repair a piece of cheese, so your original plan will not work as-is. 

One option would be to make a crusty baked cheese. For that, you make bread dough, roll out two discs like small pizza crusts, and pack the cheese in them, crimping the seam on the upper side. When you bake, any cheese getting out through a crack will stay packaged within the dough. It will still be gooey when you cut the dough, but by this point, you will be already eating it :) and the cheese inside won't get out in the oven where it dries out unpleasantly. Other crusts will probably work too (pie crust dough for example), I just said bread because this is what I am accustomed to. Only pick doughs which you can seal well, dry phylo sheets won't help, the cheese will come out if your seal is not perfect. 

If you don't want to, or can't do it with dough, you have to buy another piece of cheese for baking and use this one in a recipe without baking, for example cut up into a salad or melted into a cream soup.