Or simply cap the sewer drain line after I pull the toilet?

No, you cannot. Toilet doesn't have trap. Floor drain requires trap. Trap keeps sewer gas from entering living space. You could break the concrete, install trap and than put drain on top of it. Otherwise, just remove the toilet and plug the hole. To plug the hole, you can take old newspaper and push it inside the pipe. Mix and pour concrete over it, all the way to the top of the pipe. Or, buy a plug of the correct size and insert it into the hole.

Let us know how you did... Good luck... Milo