Since silicone's cured with a catalyst, once it's cured it's cured, and you can't correct your cut.
But, it's nonporous all the way through, as you already know, so you should be fine. There'd be no need to boil it every time (unless you're particular enough about germs to want to with all your toys)---the surface of the little cut is no different from the surface of the rest of the dildo.
I really hate it when brand new anything gets damaged. The first scratch in a paint job, the first scuff on a shoe... even worse for a cut in silicone which was never supposed to happen!