Sure you can. Since you know what the problem is, the cure cant be too bad. Before you start, go to a hardware store and buy another wax ring for the toilet. Turn the water off, and flush the toilet, then scoop out the rest of the water. When you have gotten all the water out of the bowl and the tank that you can, pull the water line off and loosen the nuts holding the toilet to the floor. They will be under the little cups at the base.
With everything clear lift the toilet straight up to remove it, now you can get to both sides of the toilet and start searching for the ball point pen. Wiggle it, shake it, until you can hear it rattle. You may get lucky and it will fall right out. You could also take the thing outside and run the garden hose up from the bottom and try to flush it out backwards. When you do get it out, then scrape all the old wax ring away and install the new one. Makr sure the toilet is lined up so you can drop it straight down on the studs. Don't overtighten the nuts or you can break the toilet. Just snug them up firmly, until the toilet doesn't rock. Hook up the water line and give it a try. Good luck.