If the goal is not to create the hole of a point always present in the sketch, this is not possible to my knowledge, we can transform the lines into construction lines, but we will have to delete the points in a hole function so that they are not included.
Edit: I assumed that the piercing assistant was used.
There is a point that is not very clear in what you explain, but most certainly clear to you.
You want to deselect the 3rd point in the sketch without deleting it... and so you delete the function to redo it with only 2 points. In conclusion, it's as if you were removing the 3rd point, isn't it?
Normally just open the function in position, select the point to be deleted and right click on it and just delete/delete and your piercing will be deselected.
If you created a sketch with three points before doing the drilling function, you end up with the sketch of the function constrained by the first sketch.
The manipulation. de Hdijoux is therefore the right one.
Unlike inventor which handles 2 types of points for the analogous function, with SW if you place a sketch entity of type point, it creates a hole at that point.
If you want to keep the position of the point, I don't see any other solution than to make a construction geometry (based on lines, arcs and circles).